RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy524
(111 letters)
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 31.5 bits (72), Expect = 0.059
Identities = 12/58 (20%), Positives = 25/58 (43%)
Query: 12 IALQTMKDRCQLLQLRLSNLEEENLKLRIDKKKSETNEKEPKESLVSKLNEEIEMLSQ 69
+ ++ L+ L E+ +L + +++ E + V +L EEIE L +
Sbjct: 13 LESYEPQEYLNKLEDTKLKLLEKEKRLLLLEEQRLEAEGLRLKREVDRLREEIERLKE 70
>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 30.8 bits (70), Expect = 0.10
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 32 EEENLKLRIDKKKSETNEKEPKESLVSKLNEEIEMLSQQKT 72
+ E L + +KK E ++E K+ + +L E IE L Q T
Sbjct: 320 DNEKLDAEVKEKKKEKKKEEKKKKQIERLEERIEKLEVQAT 360
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 30.6 bits (69), Expect = 0.11
Identities = 19/99 (19%), Positives = 44/99 (44%), Gaps = 1/99 (1%)
Query: 7 NCALQIALQTMKDRCQLLQLRLSNLE-EENLKLRIDKKKSETNEKEPKESLVSKLNEEIE 65
N ++ L+T++ + + L+ E +E L+ +K+ E E E+ ++ E ++
Sbjct: 114 NALVRAGLKTLQRVPEYMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLK 173
Query: 66 MLSQQKTQLTHHIFMVATENKQLWTKLSMLTEETNVPEQ 104
L + ++L + + E L + L +PE+
Sbjct: 174 RLEVENSRLEEMLKKLPGEVYDLKKRWDELEPGVELPEE 212
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 30.6 bits (70), Expect = 0.11
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 19 DRCQLLQLRLSNLEEENLKLRIDKKKSETNEKEPKESLVSKLNEEIEMLSQ 69
+R + L+ R S LEE+ +L K + E E E + +L E+E L
Sbjct: 1 ERLEALEERNSELEEQIRQLE-LKLRDLEAENEKLERELERLKSELEKLKS 50
Score = 25.2 bits (56), Expect = 8.1
Identities = 16/44 (36%), Positives = 28/44 (63%), Gaps = 3/44 (6%)
Query: 9 ALQIALQTMKDRCQLLQLRLSNLEEENLKLR--IDKKKSETNEK 50
AL+ ++++ + L+L+L +LE EN KL +++ KSE EK
Sbjct: 5 ALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSE-LEK 47
>gnl|CDD|225224 COG2348, COG2348, Peptidoglycan interpeptide bridge formation
enzyme [Cell wall/membrane/envelope biogenesis].
Length = 418
Score = 30.4 bits (69), Expect = 0.16
Identities = 13/76 (17%), Positives = 34/76 (44%), Gaps = 2/76 (2%)
Query: 8 CALQIALQTMKDRCQLLQLRLSNLEEENLKLRIDKKKSETNEKEPKESLVSKLNEEIEML 67
L +A + + + L L+ L E +++ K+S +EK ++ +++L ++E
Sbjct: 235 AELPLAYLDLDEYLKKLNQELAKLAAEIERVQEALKESPKSEK--AQNKLNRLQMQLEAF 292
Query: 68 SQQKTQLTHHIFMVAT 83
++ + I +
Sbjct: 293 EERIALIEEVIVLAGI 308
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 27.6 bits (62), Expect = 1.3
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 13 ALQTMKDRCQLLQLRLSNLEEE--NLKLRIDKKKSETNEKEPKESLVSKLNEEIEMLSQQ 70
AL +K R + L+ L L++ L+ +I+K K E E + L+ +L + + L +
Sbjct: 63 ALNKLKTRLEKLKKELEELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKELKKL 122
Query: 71 KTQL 74
K +L
Sbjct: 123 KAEL 126
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 26.9 bits (60), Expect = 2.0
Identities = 20/94 (21%), Positives = 42/94 (44%), Gaps = 2/94 (2%)
Query: 9 ALQIALQTMKDRCQLLQLRLSNLEEENLKLRIDKKKSETNEKEPKESLVS--KLNEEIEM 66
LQ L +++ LQ +L+ L++EN +L+ + E + ++ L +L+
Sbjct: 70 ELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIE 129
Query: 67 LSQQKTQLTHHIFMVATENKQLWTKLSMLTEETN 100
L ++ +L + + EN+ L + L E
Sbjct: 130 LDEENRELREELAELKQENEALEAENERLQENEQ 163
>gnl|CDD|232988 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. Most
phenylalanyl-tRNA synthetases are heterodimeric, with 2
alpha (pheS) and 2 beta (pheT) subunits. This model
describes the alpha subunit, which shows some similarity
to class II aminoacyl-tRNA ligases. Mitochondrial
phenylalanyl-tRNA synthetase is a single polypeptide
chain, active as a monomer, and similar to this chain
rather than to the beta chain, but excluded from this
model. An interesting feature of the alignment of all
sequences captured by this model is a deep split between
non-spirochete bacterial examples and all other
examples; supporting this split is a relative deletion
of about 50 residues in the former set between two
motifs well conserved throughout the alignment [Protein
synthesis, tRNA aminoacylation].
Length = 293
Score = 26.9 bits (60), Expect = 2.0
Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 40 IDKKKSETNEKEPKESLVSKLNEEIEMLSQQKTQLTHHIFMVATENKQLWTKLSMLTEET 99
+ K+ + ++E K +L + +NE L + T+L + E+ LW+KL T +
Sbjct: 5 LLKQLGKLTKEETKPALGALINEVKIELQDELTKLKPEL-----ESAGLWSKLKFETYDV 59
Query: 100 NVPEQSI 106
++P I
Sbjct: 60 SLPGTKI 66
>gnl|CDD|223061 PHA03369, PHA03369, capsid maturational protease; Provisional.
Length = 663
Score = 26.9 bits (59), Expect = 2.4
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 25 QLRLSNLEEENLKLRIDKKKSETNEKEPKE-SLVSKLNEEIEMLSQQKTQLTHHIFMV 81
+ +E+ R K+ E E+ + LV KL EE E L+++ H +
Sbjct: 452 NMVYPGHPQEHGHERKRKRGGELKEELIETLKLVKKLKEEQESLAKELEATAHKSEIK 509
>gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated.
Length = 313
Score = 26.5 bits (59), Expect = 3.1
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 10 LQIALQTMKDRCQLLQLRLSNLEEENLKLRIDKKKSETNEKEPKESL 56
L+ L T+K RCQ+ +L+ L +E ++ I K ++ E+E K ++
Sbjct: 133 LEQILDTIKSRCQI--YKLNRLSKEEIEKFISYKYNDIKEEEKKSAI 177
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 26.6 bits (59), Expect = 3.3
Identities = 28/99 (28%), Positives = 50/99 (50%), Gaps = 1/99 (1%)
Query: 9 ALQIALQTMKDRCQLLQLRLSNLEEENLKLRIDKKKSETNEKEPKESLVSKLNEEIEMLS 68
AL+ L+ ++ R + L+ L LEEE +L+ ++ E + +E+L +KL EEIE L
Sbjct: 727 ALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEAL-AKLKEEIEELE 785
Query: 69 QQKTQLTHHIFMVATENKQLWTKLSMLTEETNVPEQSIN 107
+++ L + + E ++ +L L E EQ
Sbjct: 786 EKRQALQEELEELEEELEEAERRLDALERELESLEQRRE 824
>gnl|CDD|237088 PRK12393, PRK12393, amidohydrolase; Provisional.
Length = 457
Score = 26.6 bits (59), Expect = 3.3
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 56 LVSKLNEEIEMLSQQKTQLTH 76
LV EEI +L+Q T + H
Sbjct: 275 LVKLDAEEIALLAQTGTGIAH 295
>gnl|CDD|191096 pfam04799, Fzo_mitofusin, fzo-like conserved region. Family of
putative transmembrane GTPase. The fzo protein is a
mediator of mitochondrial fusion. This conserved region
is also found in the human mitofusin protein.
Length = 171
Score = 26.2 bits (58), Expect = 3.4
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 2 DSTTSNCALQIALQ---TMKDRCQLLQLRLSNLEEENLKLRIDKKKSETNEKEPK 53
T+SNC+ Q+ + T CQ + + +LEEE +L + ++ ET + K
Sbjct: 93 SLTSSNCSHQVQQELASTFARLCQQVDVTSKDLEEEIAELTKEIQRLETIQSRSK 147
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 26.6 bits (59), Expect = 3.6
Identities = 23/109 (21%), Positives = 46/109 (42%), Gaps = 6/109 (5%)
Query: 9 ALQIALQTMKDRCQLLQLRLSNLEEENLKLRID------KKKSETNEKEPKESLVSKLNE 62
L+ ++ +K+ + L+ L L E L + + +S E + L E
Sbjct: 786 ELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEE 845
Query: 63 EIEMLSQQKTQLTHHIFMVATENKQLWTKLSMLTEETNVPEQSINLVKD 111
+IE LS+ L I + ++L ++L L E E+++ L++
Sbjct: 846 QIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLRS 894
>gnl|CDD|219781 pfam08287, DASH_Spc19, Spc19. Spc19 is a component of the DASH
complex. The DASH complex associates with the spindle
pole body and is important for spindle and kinetochore
integrity during cell division.
Length = 150
Score = 25.7 bits (57), Expect = 4.2
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 10 LQIALQTMKDRCQLLQLRLSNLEEENLKLRIDKKKSETNEKEPKESLVSKLNEEIEMLSQ 69
LQ T+K + +L + RLSN E + R+ K + S KL E ++ L Q
Sbjct: 80 LQREEDTLKAKYELNKGRLSNSESRSTDSRLGLNKVSDDPVNMASSTEEKL-ERLKELKQ 138
Query: 70 QKTQL 74
+K +L
Sbjct: 139 KKERL 143
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 25.6 bits (57), Expect = 5.5
Identities = 12/48 (25%), Positives = 25/48 (52%)
Query: 27 RLSNLEEENLKLRIDKKKSETNEKEPKESLVSKLNEEIEMLSQQKTQL 74
++ +++E KL I ++ + KE + +L E+I L +K +L
Sbjct: 37 EIAEIDDEIAKLGIKLSRAILKNPDKKEETLKELKEKITDLRVKKAEL 84
>gnl|CDD|224286 COG1367, COG1367, CRISPR system related protein, RAMP superfamily
[Defense mechanisms].
Length = 393
Score = 25.3 bits (55), Expect = 8.3
Identities = 9/57 (15%), Positives = 21/57 (36%), Gaps = 1/57 (1%)
Query: 36 LKLRIDKKKSETNEKE-PKESLVSKLNEEIEMLSQQKTQLTHHIFMVATENKQLWTK 91
L+++ K ++ K+ + KL ++ S+ K +L F+
Sbjct: 175 LEIKSPKLTNDYQLVISEKQEHIRKLKNKVNSSSKVKIKLLRTNFIGIPNFPCFCDY 231
>gnl|CDD|173004 PRK14538, PRK14538, putative bifunctional signaling protein/50S
ribosomal protein L9; Provisional.
Length = 838
Score = 25.2 bits (55), Expect = 8.8
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 32 EEENLKLRIDKKKSETNEKEPKESLVSKLNEEIE 65
++ENL KK E +K E L+ KL EI+
Sbjct: 727 DKENLAKIKKKKILEQEKKRNHELLMKKLKSEID 760
>gnl|CDD|240370 PTZ00342, PTZ00342, acyl-CoA synthetase; Provisional.
Length = 746
Score = 25.1 bits (55), Expect = 9.8
Identities = 10/38 (26%), Positives = 21/38 (55%)
Query: 29 SNLEEENLKLRIDKKKSETNEKEPKESLVSKLNEEIEM 66
N EE+N ++ ++ N++E K + +S E+I +
Sbjct: 218 INKEEKNNGSNVNNNGNKNNKEEQKGNDLSNELEDISL 255
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
0.308 0.122 0.317
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: 4,822,730
Number of extensions: 380095
Number of successful extensions: 651
Number of sequences better than 10.0: 1
Number of HSP's gapped: 630
Number of HSP's successfully gapped: 146
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.2 bits)