RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11028
(136 letters)
>gnl|CDD|216598 pfam01602, Adaptin_N, Adaptin N terminal region. This family
consists of the N terminal region of various alpha, beta
and gamma subunits of the AP-1, AP-2 and AP-3 adaptor
protein complexes. The adaptor protein (AP) complexes
are involved in the formation of clathrin-coated pits
and vesicles. The N-terminal region of the various
adaptor proteins (APs) is constant by comparison to the
C-terminal which is variable within members of the AP-2
family; and it has been proposed that this constant
region interacts with another uniform component of the
coated vesicles.
Length = 522
Score = 116 bits (292), Expect = 2e-31
Identities = 47/119 (39%), Positives = 68/119 (57%), Gaps = 6/119 (5%)
Query: 8 LTSTKPYLRKKAVLMMYKVFLKFPDALRPA-FPRLKEKLEDPDSGVQSAAVNVVCELARK 66
L PY+RKKA L + K++ K PD +R P LKE L D D GV SAAV ++ E+ RK
Sbjct: 122 LVDRDPYVRKKAALAILKLYRKDPDLVRDFLVPELKELLSDKDPGVVSAAVALLYEI-RK 180
Query: 67 NPKNY-LSLAPVFFKLMT---TSSNNWMLIKIIKLFGALTPLEPRLGKKLIEPLTNLIH 121
N + Y L P+ + + T N W+ +KI++L P +PR K+L+E + NL+
Sbjct: 181 NDRLYLNKLLPLLVRRLCNLLTVCNPWLQVKILRLLTRYAPQDPREPKELLEDILNLLQ 239
Score = 31.0 bits (71), Expect = 0.16
Identities = 13/70 (18%), Positives = 24/70 (34%)
Query: 45 LEDPDSGVQSAAVNVVCELARKNPKNYLSLAPVFFKLMTTSSNNWMLIKIIKLFGALTPL 104
L S V V V+ ++ RK P+ + +L+ + + + G L
Sbjct: 384 LSLAGSYVVDEIVEVIRDIIRKYPELREYILEHLCELLEDIESPEARAAALWILGEYGEL 443
Query: 105 EPRLGKKLIE 114
P L+
Sbjct: 444 IPNSPSDLLR 453
>gnl|CDD|221731 pfam12717, Cnd1, non-SMC mitotic condensation complex subunit 1.
The three non-SMC (structural maintenance of
chromosomes) subunits of the mitotic condensation
complex are Cnd1-3. The whole complex is essential for
viability and the condensing of chromosomes in mitosis.
Length = 171
Score = 32.9 bits (76), Expect = 0.022
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 8 LTSTKPYLRKKAVLMMYKVFL----KFPDALRPAFPRLKEKLEDPDSGVQSAAVNVVCEL 63
L PY+RK A+L++ + L K L + L D D +++ A + EL
Sbjct: 34 LRDEDPYVRKTALLVLTHLILNDMVKVKGQLFLEMLKC---LVDEDPEIRALAKSFFSEL 90
Query: 64 ARKNPKN 70
+KNP
Sbjct: 91 LKKNPNL 97
>gnl|CDD|227427 COG5096, COG5096, Vesicle coat complex, various subunits
[Intracellular trafficking and secretion].
Length = 757
Score = 31.2 bits (71), Expect = 0.12
Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 3/102 (2%)
Query: 8 LTSTKPYLRKKAVLMMYKVFLKFPDALRPAFP--RLKEKLEDPDSGVQSAAVNVVCELAR 65
LT Y+RK A L + K++ D LKE + D D V + A+ + E+
Sbjct: 136 LTDPHAYVRKTAALAVAKLYRLDKDLYHELGLIDILKELVADSDPIVIANALASLAEIDP 195
Query: 66 KNPKNYLSLAPVFFK-LMTTSSNNWMLIKIIKLFGALTPLEP 106
+ Y + L S + ++ + LT P
Sbjct: 196 ELAHGYSLEVILRIPQLDLLSLSVSTEWLLLIILEVLTERVP 237
>gnl|CDD|205691 pfam13513, HEAT_EZ, HEAT-like repeat. The HEAT repeat family is
related to armadillo/beta-catenin-like repeats (see
pfam00514). These EZ repeats are found in subunits of
cyanobacterial phycocyanin lyase and other proteins and
probably carry out a scaffolding role.
Length = 55
Score = 29.0 bits (65), Expect = 0.14
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 13 PYLRKKAVLMMYKVFLKFPDALRP----AFPRLKEKLEDPDSGVQSAAV 57
+R+ A L + + P+ LRP P L L+D D V+ AA
Sbjct: 1 WEVREAAALALGALAGGGPELLRPAVPELLPALLPLLKDDDDEVREAAA 49
>gnl|CDD|237987 cd00020, ARM, Armadillo/beta-catenin-like repeats. An approximately
40 amino acid long tandemly repeated sequence motif
first identified in the Drosophila segment polarity gene
armadillo; these repeats were also found in the
mammalian armadillo homolog beta-catenin, the junctional
plaque protein plakoglobin, the adenomatous polyposis
coli (APC) tumor suppressor protein, and a number of
other proteins. ARM has been implicated in mediating
protein-protein interactions, but no common features
among the target proteins recognized by the ARM repeats
have been identified; related to the HEAT domain; three
consecutive copies of the repeat are represented by this
alignment model.
Length = 120
Score = 30.0 bits (68), Expect = 0.20
Identities = 18/106 (16%), Positives = 31/106 (29%), Gaps = 15/106 (14%)
Query: 39 PRLKEKLEDPDSGVQSAAVNVVCELARKNPKNYLSLA-----PVFFKLMTTSSNNW---- 89
P L L D VQ A + L+ N N ++ P +L+ +
Sbjct: 10 PALVSLLSSSDENVQREAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLKSEDEEVVKAA 69
Query: 90 -MLIKIIKLFGALTPLEPRLGKKLIEPLTNLIH----RIISLSCWT 130
++ + G L + L NL+ I +
Sbjct: 70 LWALRNL-AAGPEDNKLIVLEAGGVPKLVNLLDSSNEDIQKNATGA 114
>gnl|CDD|237417 PRK13533, PRK13533, 7-cyano-7-deazaguanine tRNA-ribosyltransferase;
Provisional.
Length = 487
Score = 29.5 bits (67), Expect = 0.54
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 1/66 (1%)
Query: 10 STKPYLRKKAVLMMYKVFLK-FPDALRPAFPRLKEKLEDPDSGVQSAAVNVVCELARKNP 68
KP + ++ +K FP L +P +E+ E+ D +AA + L NP
Sbjct: 398 GDKPENDSEDDVLFFKPPFGPFPPELSETYPLSQEEPEEIDEEAIAAAAEGLARLLEANP 457
Query: 69 KNYLSL 74
+L
Sbjct: 458 YAKFTL 463
>gnl|CDD|224331 COG1413, COG1413, FOG: HEAT repeat [Energy production and
conversion].
Length = 335
Score = 29.1 bits (65), Expect = 0.60
Identities = 27/115 (23%), Positives = 42/115 (36%), Gaps = 14/115 (12%)
Query: 7 YLTSTKPYLRKKAVLMMYKVFLKFPDALRPAFPRLKEKLEDPDSGVQSAAVNVVCELARK 66
L +R A V L + A P L+E L D D V+ AA + + EL
Sbjct: 51 LLEDEDLLVRLSAA-----VALGELGSEE-AVPLLRELLSDEDPRVRDAAADALGEL--G 102
Query: 67 NPKNYLSLAPVFFKLMTTSSNNWMLIKIIKLFGALTPLEPRLGKKLIEPLTNLIH 121
+P+ P +L+ N + + G L + R L+E L +
Sbjct: 103 DPE----AVPPLVELLENDENEGVRAAAARALGKLG--DERALDPLLEALQDEDS 151
Score = 28.0 bits (62), Expect = 1.7
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 7/66 (10%)
Query: 37 AFPRLKEKLEDPDSGVQSAAVNVVCELARKNPKNYLSLAPVFFKLMTTSSNNW-MLIKII 95
A P L E LED D+ V+ AA + + +L +N + A + K + S + + +
Sbjct: 181 AIPLLIELLEDEDADVRRAAASALGQLGSENVE----AADLLVKAL--SDESLEVRKAAL 234
Query: 96 KLFGAL 101
G +
Sbjct: 235 LALGEI 240
>gnl|CDD|189015 cd09608, M3B_PepF_3, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 538
Score = 28.6 bits (65), Expect = 0.91
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 4 YFIYLTSTKPYLRKKAVLMMYKVFLKF 30
Y L S +RK+A +YK +L+F
Sbjct: 146 YSRLLESKDREVRKEAFEALYKTYLQF 172
>gnl|CDD|222285 pfam13646, HEAT_2, HEAT repeats. This family includes multiple
HEAT repeats.
Length = 88
Score = 27.7 bits (62), Expect = 0.92
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 6/53 (11%)
Query: 6 IYLTSTKPYLRKKAVLMMYKVFLKFPDALRPAFPRLKEKLEDPDSGVQSAAVN 58
L+ P +R A + + L P+AL P L E L+DPD V+ AA
Sbjct: 7 ALLSDPDPEVRAAAARALGE--LGDPEAL----PALLELLKDPDPEVRRAAAE 53
>gnl|CDD|234308 TIGR03682, arCOG04112, diphthamide biosynthesis enzyme Dph2.
Members of this family are the archaeal protein Dph2,
members of the universal archaeal protein family
designated arCOG04112. The chemical function of this
protein is analogous to the radical SAM family
(pfam04055), although the sequence is not homologous.
The chemistry involves [4Fe-4S]-aided formation of a
3-amino-3-carboxypropyl radical rather than the
canonical 5'-deoxyadenosyl radical of the radical SAM
family.
Length = 308
Score = 28.4 bits (64), Expect = 1.1
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 25 KVFLKFPDALRPAFPRLKEKLEDPDSGV 52
+V L+ P+ L+ + +KLE+ V
Sbjct: 4 RVLLQAPEGLKRRAFEIAQKLEEKGYEV 31
>gnl|CDD|202500 pfam02985, HEAT, HEAT repeat. The HEAT repeat family is related
to armadillo/beta-catenin-like repeats (see pfam00514).
Length = 31
Score = 25.2 bits (56), Expect = 2.5
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 38 FPRLKEKLEDPDSGVQSAAVNVVCELARK 66
P L E L DPD V+ AA + LA
Sbjct: 2 LPLLLELLNDPDPEVREAAAEALGALAEV 30
>gnl|CDD|148003 pfam06139, BphX, BphX-like. Family of bacterial proteins located
in the phenyl dioxygenase (bph) operon. The function of
this family is unknown.
Length = 136
Score = 26.2 bits (58), Expect = 5.0
Identities = 23/80 (28%), Positives = 32/80 (40%), Gaps = 12/80 (15%)
Query: 4 YFIYLTSTKPYLRKKAVLMMYKVFLKFPDALRPAFPRLKEKLEDPDS----GVQSAAVNV 59
Y + L T P+ MMY D P F L+ D+ G+Q A+ V
Sbjct: 15 YLLNLVGTLPFSSLGLFGMMYPGVE--LDVGTPIFTLLQ------DAWAVVGLQLGAIGV 66
Query: 60 VCELARKNPKNYLSLAPVFF 79
V ++P YL+L PV
Sbjct: 67 VALWGARDPLRYLALIPVVI 86
>gnl|CDD|227683 COG5395, COG5395, Predicted membrane protein [Function unknown].
Length = 131
Score = 25.9 bits (57), Expect = 5.5
Identities = 13/55 (23%), Positives = 25/55 (45%)
Query: 50 SGVQSAAVNVVCELARKNPKNYLSLAPVFFKLMTTSSNNWMLIKIIKLFGALTPL 104
S + + A+ V + K + L V+ LM ++ + + I I L G +P+
Sbjct: 19 SAITALALGAVLMMRVKGTTLHRLLGRVWVALMGATAVSSLFIHEINLHGGFSPI 73
>gnl|CDD|227565 COG5240, SEC21, Vesicle coat complex COPI, gamma subunit
[Intracellular trafficking and secretion].
Length = 898
Score = 26.5 bits (58), Expect = 5.7
Identities = 17/95 (17%), Positives = 37/95 (38%), Gaps = 7/95 (7%)
Query: 31 PDALRPAFPRLKEKLEDPDSGVQSAAVNVVCELARKNPKNYLSLAPVFFKLMTTSSNNWM 90
+ L+ L+ ++ +A+ ++ +LA K P+ L++ +
Sbjct: 298 SQFVDQTVSSLRTFLKSTRVVLRFSAMRILNQLAMKYPQKVSVCNKEVESLISDENRT-- 355
Query: 91 LIKIIKLFGALTPLEPRLGKKLIEPLTNLIHRIIS 125
I + A+T L ++ I+ L NLI +
Sbjct: 356 ----ISTY-AITTLLKTGTEETIDRLVNLIPSFVH 385
>gnl|CDD|215640 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 26.5 bits (58), Expect = 5.8
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 79 FKLMTTSSNNWMLIKIIKLFGAL 101
F L TSSN W+ I++ L G +
Sbjct: 1125 FTLANTSSNRWLTIRLETLGGVM 1147
>gnl|CDD|216105 pfam00761, Polyoma_coat2, Polyomavirus coat protein.
Length = 322
Score = 26.0 bits (57), Expect = 7.3
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 85 SSNNWMLIKIIKLFGALTP 103
+ +WML ++ L+G LTP
Sbjct: 289 VAPDWMLPLLLGLYGDLTP 307
>gnl|CDD|227441 COG5110, RPN1, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 881
Score = 26.0 bits (57), Expect = 8.8
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 7/49 (14%)
Query: 41 LKEKLEDPDSGVQSAAVNVVCELARKN-------PKNYLSLAPVFFKLM 82
L E+++DPD +Q+ ++N++ E+ + + PK L P + L+
Sbjct: 52 LVERIQDPDIDLQNNSLNMLKEVIKSSTSSMTAVPKPLKFLRPNYLDLL 100
>gnl|CDD|147573 pfam05461, ApoL, Apolipoprotein L. Apo L belongs to the high
density lipoprotein family that plays a central role in
cholesterol transport. The cholesterol content of
membranes is important in cellular processes such as
modulating gene transcription and signal transduction
both in the adult brain and during neurodevelopment.
There are six apo L genes located in close proximity to
each other on chromosome 22q12 in humans. 22q12 is a
confirmed high-susceptibility locus for schizophrenia
and close to the region associated with
velocardiofacial syndrome that includes symptoms of
schizophrenia.
Length = 313
Score = 25.8 bits (57), Expect = 8.9
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 7/28 (25%)
Query: 20 VLMMYKVFLKFPDALRPAFPRLKEKLED 47
+ FLK FPRLK +LE+
Sbjct: 56 DQQDRERFLK-------EFPRLKAELEE 76
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
0.324 0.139 0.422
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,050,157
Number of extensions: 626631
Number of successful extensions: 840
Number of sequences better than 10.0: 1
Number of HSP's gapped: 835
Number of HSP's successfully gapped: 37
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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: 54 (24.6 bits)