RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13031
(477 letters)
>gnl|CDD|217859 pfam04045, P34-Arc, Arp2/3 complex, 34 kD subunit p34-Arc. Arp2/3
protein complex has been implicated in the control of
actin polymerisation in cells. The human complex
consists of seven subunits which include the actin
related Arp2 and Arp3, and five others referred to as
p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. This
family represents the p34-Arc subunit.
Length = 240
Score = 311 bits (798), Expect = e-104
Identities = 132/299 (44%), Positives = 175/299 (58%), Gaps = 67/299 (22%)
Query: 178 SISLKFYKELEEHGADELLRREYGSLL-SEPEPGYNVSVLINLEDVP-SNWEEIVKKIGL 235
S+SLK + +L ++GA+ELL+REYG+ L +PEPGY+VS+LI+LE++P EE+++KI L
Sbjct: 3 SVSLKCWPDLVKYGAEELLKREYGTYLGVKPEPGYDVSLLIDLEELPADEREELIEKIAL 62
Query: 236 SRLQCVRTHQPGRCALKLGGDSQENRYVEAKADRVTVVFSTVFRDEDDVIIGKVFMQEFK 295
LK + F K F ++
Sbjct: 63 ---------------LK------------------RNCMAAPFE--------KAF-EKQA 80
Query: 296 EGRRASHTAPQVLFSHKEPPLELRNTDARQGDNIGYITFGKYVEAKADRVTVVFSTVFRD 355
E + + + R + I Y++ DRVTV+FSTVF+D
Sbjct: 81 ELAEEAEGEEVAVIHY------------RDDETI-------YIKPSFDRVTVIFSTVFKD 121
Query: 356 EDDVIIGKVFMQEFKEGRRAS-HTAPQVLFSHKEPPLELRNT--DARQGDNIGYITFVLF 412
E D IIGKVF+QEF + RR S TAPQVLFSHKEPPLEL+ A+ GDN+GY+TFVLF
Sbjct: 122 ETDKIIGKVFLQEFVDARRRSRQTAPQVLFSHKEPPLELQGVPGAAKAGDNVGYVTFVLF 181
Query: 413 PRH-TNRVARENTINLIHMFRDYLHYHIKCSKAYIHSRMRAKTSDFLKVLNRARPEVKN 470
PRH R+NTI+LI FR+YLHYHIKCSKAY+HSRMR + ++FLKVLNRA+PE K+
Sbjct: 182 PRHLVTPKRRDNTISLIQTFRNYLHYHIKCSKAYMHSRMRNRVAEFLKVLNRAKPEPKD 240
>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein.
Length = 96
Score = 75.8 bits (187), Expect = 5e-17
Identities = 22/85 (25%), Positives = 35/85 (41%), Gaps = 3/85 (3%)
Query: 35 SAAGATGAFVGTPAEVALIRMTADGRLPPAERRNYKNVFHALYRMTSQEGVLTLWRGTIP 94
AGA A V P +V R+ R YK + ++ +EG+ L++G +P
Sbjct: 13 GIAGAIAATVTYPLDVVKTRLQ---SSAAGGSRKYKGILDCFKKIYKEEGIRGLYKGLLP 69
Query: 95 TMGRAMVVNAAQLASYSQAKQFLLS 119
+ R A +Y K+ LL
Sbjct: 70 NLLRVAPAAAIYFGTYETLKKLLLK 94
Score = 44.6 bits (106), Expect = 5e-06
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 126 NIFCFFVSSMISAFITTVASMPVDIAKTRIQNMKTIDGKPEFKGAFDVLGKT 177
+ ++ I+ I + P+D+ KTR+Q G ++KG D K
Sbjct: 4 SFLASLLAGGIAGAIAATVTYPLDVVKTRLQ-SSAAGGSRKYKGILDCFKKI 54
>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
Provisional.
Length = 300
Score = 48.6 bits (116), Expect = 3e-06
Identities = 33/117 (28%), Positives = 56/117 (47%), Gaps = 11/117 (9%)
Query: 69 YKNVFHALYRMTSQEGVLTLWRGTIPTMGRAMVVNAAQLASYSQAKQFLLSL--SYFEEN 126
Y + + R++ ++GVL+LWRG + R A A K + ++ Y ++
Sbjct: 52 YSGIVNCFRRVSKEQGVLSLWRGNTANVIRYFPTQAFNFA----FKDYFKNMFPKYNQKT 107
Query: 127 IFC-FFVSSMISAFITTVASM----PVDIAKTRIQNMKTIDGKPEFKGAFDVLGKTS 178
F FF +++S + +S+ P+D A+TR+ + G EF G FD L K S
Sbjct: 108 DFWKFFGVNILSGGLAGASSLLIVYPLDFARTRLASDIGKGGDREFTGLFDCLMKIS 164
Score = 42.4 bits (100), Expect = 3e-04
Identities = 41/178 (23%), Positives = 73/178 (41%), Gaps = 17/178 (9%)
Query: 1 MFSEYNTEAHILKPESVDITIADFDGVLFHISNLSAAGATGAFVGTPAEVALIRMTADGR 60
MF +YN + K F GV +I + AGA+ + P + A R+ +D
Sbjct: 99 MFPKYNQKTDFWK----------FFGV--NILSGGLAGASSLLIVYPLDFARTRLASD-- 144
Query: 61 LPPAERRNYKNVFHALYRMTSQEGVLTLWRGTIPTMGRAMVVNAAQLASYSQAKQFLLSL 120
+ R + +F L +++ Q G L+L++G ++ +V A Y AK L
Sbjct: 145 IGKGGDREFTGLFDCLMKISKQTGFLSLYQGFGVSVQGIIVYRGAYFGLYDSAKALLFGN 204
Query: 121 SYFEENIFCFFVSSMISAFITTVASMPVDIAKTRIQNMKTIDGKPE--FKGAFDVLGK 176
++ + V+ ++ + + S P D + R+ M K E + G D K
Sbjct: 205 DKNTNILYKWAVAQTVTI-LAGLISYPFDTVRRRMMMMSGRKAKSEIQYTGTLDCWKK 261
>gnl|CDD|221239 pfam11812, DUF3333, Domain of unknown function (DUF3333). This
family of proteins are functionally uncharacterized.
This family is only found in bacteria. This presumed
domain is typically between 116 to 159 amino acids in
length.
Length = 155
Score = 30.7 bits (70), Expect = 0.96
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 8/82 (9%)
Query: 129 CFFVSSMIS----AFITTVASMPVDIAKTRIQNMKTIDGKPEFKGAFDVLGKTSISLKFY 184
+ S++S AF T ++ V + + + DG + K + I
Sbjct: 31 VILLGSIVSNGYGAFQQTEITLEVTLDEEVLD----PDGNRDPKKLSTANYRPLIKDALE 86
Query: 185 KELEEHGADELLRREYGSLLSE 206
+ L E G LR + SL+SE
Sbjct: 87 ELLPEVGDRSDLRSDLYSLISE 108
>gnl|CDD|213529 TIGR00423, TIGR00423, radical SAM domain protein, CofH subfamily.
This protein family includes the CofH protein of
coenzyme F(420) biosynthesis from Methanocaldococcus
jannaschii, but appears to hit genomes more broadly than
just the subset that make coenzyme F(420), so that
narrower group is being built as a separate family
[Hypothetical proteins, Conserved].
Length = 309
Score = 29.7 bits (67), Expect = 3.3
Identities = 16/50 (32%), Positives = 19/50 (38%), Gaps = 2/50 (4%)
Query: 23 DFDGVLFHISNLSAAGATGAFVGTPAEVALIRMTADGRLPPAERRNYKNV 72
D G L + AAGA T E LI D PA+R N+
Sbjct: 261 DLGGTLMEENISKAAGAKSGVGLTVEE--LIEAIKDAGRVPAQRDTLYNI 308
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 29.9 bits (68), Expect = 3.4
Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 9/69 (13%)
Query: 171 FDVL--GKTSISLKFYKELEEH-----GADELLRREYGSLLSEP--EPGYNVSVLINLED 221
FD L KTS + EL H ADEL + G+LLS P + +N+ L+
Sbjct: 259 FDYLKGEKTSFTFYVSNELNIHRTKLENADELYNKHLGNLLSPPCLDDKFNLPELVFHTF 318
Query: 222 VPSNWEEIV 230
+IV
Sbjct: 319 TIKEKTDIV 327
>gnl|CDD|237717 PRK14455, PRK14455, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 356
Score = 28.8 bits (65), Expect = 6.7
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 181 LKFYKELEEHGADELLRREYGS 202
F L+++G + +RRE+G+
Sbjct: 316 FAFEDTLKKNGVNCTIRREHGT 337
>gnl|CDD|235148 PRK03655, PRK03655, putative ion channel protein; Provisional.
Length = 414
Score = 28.9 bits (65), Expect = 7.1
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 34 LSAAGATGAFVGTPAEVALI 53
L++AG GA GTP ALI
Sbjct: 150 LASAGTIGALFGTPVAAALI 169
>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 = 28.5 bits (64), Expect = 9.4
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 164 KPEFKGAFDVLGKTSISLKFYKELE 188
KP K FD LGK SI ++Y E+E
Sbjct: 155 KPPNKVIFDFLGKDSI--RYYNEVE 177
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
0.321 0.135 0.391
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: 24,745,554
Number of extensions: 2460388
Number of successful extensions: 2246
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2237
Number of HSP's successfully gapped: 17
Length of query: 477
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 376
Effective length of database: 6,457,848
Effective search space: 2428150848
Effective search space used: 2428150848
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: 61 (27.3 bits)