RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3215
(186 letters)
>gnl|CDD|238103 cd00176, SPEC, Spectrin repeats, found in several proteins involved
in cytoskeletal structure; family members include
spectrin, alpha-actinin and dystrophin; the spectrin
repeat forms a three helix bundle with the second helix
interrupted by proline in some sequences; the repeats
are independent folding units; tandem repeats are found
in differing numbers and arrange in an antiparallel
manner to form dimers; the repeats are defined by a
characteristic tryptophan (W) residue in helix A and a
leucine (L) at the carboxyl end of helix C and separated
by a linker of 5 residues; two copies of the repeat are
present here.
Length = 213
Score = 59.0 bits (143), Expect = 4e-11
Identities = 30/131 (22%), Positives = 64/131 (48%), Gaps = 3/131 (2%)
Query: 35 QRYDAKRQEVDGWLTRMENRMQRMNPVGYTADVLEVQLREQKSIHADLHQFKQQIVLFNQ 94
Q++ E++ WL+ E + + + +E L++ +++ A+L ++++ N+
Sbjct: 3 QQFLRDADELEAWLSEKEELLSSTDYGD-DLESVEALLKKHEALEAELAAHEERVEALNE 61
Query: 95 LTQKLISVYQHDDTTRVKKITEQVNQRYNNLNTSIINRGKALNSAMSSLQNFDKSIDNFL 154
L ++LI H D +++ E++NQR+ L R + L A+ Q F + D+
Sbjct: 62 LGEQLIEEG-HPDAEEIQERLEELNQRWEELRELAEERRQRLEEALDLQQFFRDA-DDLE 119
Query: 155 AWLSEAESTME 165
WL E E+ +
Sbjct: 120 QWLEEKEAALA 130
Score = 56.3 bits (136), Expect = 5e-10
Identities = 28/139 (20%), Positives = 63/139 (45%), Gaps = 2/139 (1%)
Query: 2 ILHKITKLREHWDETNNKVMARKTQLDSMLSDSQRYDAKRQEVDGWLTRMENRMQRMNPV 61
I ++ +L + W+E R+ +L+ L Q + +++ WL E + +
Sbjct: 77 IQERLEELNQRWEELRELAEERRQRLEEALDLQQFFRDAD-DLEQWLEEKEAALASE-DL 134
Query: 62 GYTADVLEVQLREQKSIHADLHQFKQQIVLFNQLTQKLISVYQHDDTTRVKKITEQVNQR 121
G + +E L++ K + +L + ++ N+L ++L+ D +++ E++N+R
Sbjct: 135 GKDLESVEELLKKHKELEEELEAHEPRLKSLNELAEELLEEGHPDADEEIEEKLEELNER 194
Query: 122 YNNLNTSIINRGKALNSAM 140
+ L R K L A+
Sbjct: 195 WEELLELAEERQKKLEEAL 213
>gnl|CDD|197544 smart00150, SPEC, Spectrin repeats.
Length = 101
Score = 46.6 bits (111), Expect = 2e-07
Identities = 22/103 (21%), Positives = 50/103 (48%), Gaps = 2/103 (1%)
Query: 35 QRYDAKRQEVDGWLTRMENRMQRMNPVGYTADVLEVQLREQKSIHADLHQFKQQIVLFNQ 94
Q++ E++ WL E + +G + +E L++ ++ A+L ++++ N+
Sbjct: 1 QQFLRDADELEAWLEEKEQLLASE-DLGKDLESVEALLKKHEAFEAELEAHEERVEALNE 59
Query: 95 LTQKLISVYQHDDTTRVKKITEQVNQRYNNLNTSIINRGKALN 137
L ++LI H D +++ E++N+R+ L R + L
Sbjct: 60 LGEQLIEE-GHPDAEEIEERLEELNERWEELKELAEERRQKLE 101
>gnl|CDD|215918 pfam00435, Spectrin, Spectrin repeat. Spectrin repeat-domains are
found in several proteins involved in cytoskeletal
structure. These include spectrin, alpha-actinin and
dystrophin. The sequence repeat used in this family is
taken from the structural repeat in reference. The
spectrin domain- repeat forms a three helix bundle. The
second helix is interrupted by proline in some
sequences. The repeats are defined by a characteristic
tryptophan (W) residue at position 17 in helix A and a
leucine (L) at 2 residues from the carboxyl end of helix
C. Although the domain occurs in ultiple repeats along
sequences, the domains are actually stable on their own
- ie they act, biophysically, like domains rather than
repeats that along function when aggregated.
Length = 105
Score = 41.5 bits (98), Expect = 2e-05
Identities = 20/102 (19%), Positives = 50/102 (49%), Gaps = 2/102 (1%)
Query: 35 QRYDAKRQEVDGWLTRMENRMQRMNPVGYTADVLEVQLREQKSIHADLHQFKQQIVLFNQ 94
Q++ +++ W+ E + G + ++ L++ K++ A+L + ++ N+
Sbjct: 4 QQFFRDADDLESWIEEKEALLS-SEDYGKDLESVQALLKKHKALEAELAAHQDRVEALNE 62
Query: 95 LTQKLISVYQHDDTTRVKKITEQVNQRYNNLNTSIINRGKAL 136
L +KLI+ H + +++ E++N+R+ L R + L
Sbjct: 63 LAEKLIA-EGHYASEEIQERLEELNERWEQLLELAAERKQKL 103
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it but
also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 30.4 bits (69), Expect = 0.58
Identities = 24/95 (25%), Positives = 44/95 (46%), Gaps = 5/95 (5%)
Query: 90 VLFNQLTQKLISVYQHDDTTRVKKITEQVN-QRYNNLNTSIINRGKALNSAMSSLQNFDK 148
V+ Q+ +K + + D+ + E ++ +N N ++ +GK SA+ L K
Sbjct: 1027 VIVRQMLRK-VRITDSGDSNLL--PGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITK 1083
Query: 149 SIDNFLAWLSEAESTMECVEVETDRQAEKQSTPLL 183
+ N ++LS A S E +V TD + + LL
Sbjct: 1084 ASLNTESFLSAA-SFQETTKVLTDAAIKGKVDYLL 1117
>gnl|CDD|189014 cd09607, M3B_PepF_2, 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 = 581
Score = 29.8 bits (68), Expect = 0.96
Identities = 22/99 (22%), Positives = 34/99 (34%), Gaps = 15/99 (15%)
Query: 78 IHADLHQFKQQIVLFNQLTQKLISVYQHDDTTRVKKIT--EQVNQRYNNLNTSIINRGKA 135
DL + KQ I L L+ + T IT +++ + L + A
Sbjct: 15 FQEDLKKLKQLIDELKSLLDALLPSDEDAVETLEALITLLQELLELLRTLGAFVSCLLSA 74
Query: 136 -------------LNSAMSSLQNFDKSIDNFLAWLSEAE 161
LN +SL+ +D LA LSE +
Sbjct: 75 DTTDEEAQALLSQLNQLSASLEQLLTLLDKKLAALSEED 113
>gnl|CDD|240319 PTZ00226, PTZ00226, fumarate hydratase; Provisional.
Length = 570
Score = 29.6 bits (67), Expect = 1.1
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 14/65 (21%)
Query: 47 WLTRMENRMQRMNPVGYTADVLEVQLREQKSIHADLHQFKQQIVLFNQLTQKLISVYQHD 106
+L ++E +P Y D+ E L + + DL+Q ++I K +S ++
Sbjct: 363 YLEQLE-----HDPAQYLPDITEDDLSKTPVVKIDLNQPMEEI-------LKQLS--KYP 408
Query: 107 DTTRV 111
TR+
Sbjct: 409 VKTRL 413
>gnl|CDD|216597 pfam01601, Corona_S2, Coronavirus S2 glycoprotein. The coronavirus
spike glycoprotein forms the characteristic 'corona'
after which the group is named. The Spike glycoprotein
is translated as a large polypeptide that is
subsequently cleaved to S1 pfam01600 and S2.
Length = 609
Score = 29.2 bits (66), Expect = 1.3
Identities = 29/121 (23%), Positives = 46/121 (38%), Gaps = 34/121 (28%)
Query: 57 RMNPVGYTADVLEVQLREQKSIHADLHQFKQQIVLFNQLTQKLISVYQHDDTTRVKKITE 116
R+N VG T DVL QK I F + + + + + + KI +
Sbjct: 235 RLNYVGLTTDVL---QENQKLIAN---SFNKAL---GNIQDGFTTT-----ASALSKIQD 280
Query: 117 QVNQRYNNLNTSIINRGKALNSAMSSLQ-NFD---KSIDNFLAWLSEAESTMECVEVETD 172
VNQ+ G+AL+ + L NF SI + + L E+ + + D
Sbjct: 281 VVNQQ-----------GQALSQLTNQLSNNFGAISSSIQDIYSRLDALEA-----DAQVD 324
Query: 173 R 173
R
Sbjct: 325 R 325
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 29.3 bits (66), Expect = 1.3
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 16 TNNKVMARKTQLDSMLSDSQRYDAK 40
TNN V+ T++ LSD +++DAK
Sbjct: 127 TNNHVVDNATKIKVQLSDGRKFDAK 151
>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed.
Length = 438
Score = 29.0 bits (66), Expect = 1.6
Identities = 19/131 (14%), Positives = 53/131 (40%), Gaps = 17/131 (12%)
Query: 16 TNNKVMARKTQLDSML------SDSQRYDAKRQEVDGWLTRMENRMQRMNPVGYTADVLE 69
++ ++ +LD + S + ++Q +D R++ ++R +
Sbjct: 280 MRRRLEQKRQRLDQLARRLKFQSPERLLAQQQQRLDRLQQRLQRALERRLRLAKQRLERL 339
Query: 70 VQLREQKSIHADLHQFKQQIVLFNQLTQKLISVYQHDDTTRVKKITEQVNQRYNNLNT-- 127
Q +Q++ + + +Q++ QL Q+L + ++K+ +++ L
Sbjct: 340 SQRLQQQNPQRRIERAQQRL---EQLEQRLRRAMRR----QLKRKRQRLEALAQQLEALS 392
Query: 128 --SIINRGKAL 136
+ + RG A+
Sbjct: 393 PLATLARGYAI 403
>gnl|CDD|224241 COG1322, COG1322, Predicted nuclease of restriction
endonuclease-like fold, RmuC family [General function
prediction only].
Length = 448
Score = 28.9 bits (65), Expect = 1.6
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 68 LEVQLREQKSIH-ADLHQFKQQIVLFNQLTQKLISVYQHDDTTRVKKITEQVNQRYNNLN 126
L +L E K+ L Q ++Q+ L + +L S +Q +I E++N+R LN
Sbjct: 71 LIQELNELKARLQQQLLQSREQLQLLIESLAQLSSEFQE----LANEIFEELNRRLAELN 126
Query: 127 TSIINR 132
+ +
Sbjct: 127 QQNLKQ 132
>gnl|CDD|113849 pfam05094, LEF-9, Late expression factor 9 (LEF-9). Late
expression factor 9 (LEF-9) is one of the primary
components of RNA polymerase produced by baculoviruses.
LEF-9 is homologous to the largest beta-subunit of
prokaryotic DNA-directed RNA polymerase.
Length = 487
Score = 28.2 bits (63), Expect = 2.6
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 76 KSIHADLHQFKQQIVLFNQLTQKLISVYQHDD 107
K++ ADL + K FN L ++LI+VYQ +D
Sbjct: 37 KNLIADLKKNK--CNYFNSLIEQLINVYQEND 66
>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 = 28.1 bits (63), Expect = 3.7
Identities = 15/113 (13%), Positives = 44/113 (38%), Gaps = 7/113 (6%)
Query: 22 ARKTQLDSMLSDSQRYDAKRQEVDGWLTRMENR----MQRMNPVGYTADVLEVQLREQKS 77
RK +L++ + Y ++++ + + E+ ++ + + T + +
Sbjct: 267 ERKAELEAHFDEE--YQELIEQLEELIDKYESHIEKALEELESILDTEKENSEFKLDVEE 324
Query: 78 IHADLHQFKQQI-VLFNQLTQKLISVYQHDDTTRVKKITEQVNQRYNNLNTSI 129
+ A L ++ + +L +KL + + + E +N + +N I
Sbjct: 325 LKALLEALEEILEKNLQKLEEKLKDPSTSIELESITDLIESINDIIDAINELI 377
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 28.0 bits (63), Expect = 3.7
Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 23/97 (23%)
Query: 7 TKLREHWDE--TNNKVMARKTQLDSMLSDSQRYDAKRQEVDGWLTRMENRMQRMNPVGYT 64
+LR+ + N+V+A L S YDAKRQ + Q + +G
Sbjct: 1006 EQLRQAQAQLAQYNQVLA---SLKS------SYDAKRQMLQ-------ELKQELQDLGVP 1049
Query: 65 ADV-LEVQLREQKS-IHADLHQFKQQIVLFNQLTQKL 99
AD E + R ++ +HA L + + NQL ++L
Sbjct: 1050 ADSGAEERARARRDELHARLSANRSRR---NQLEKQL 1083
>gnl|CDD|217744 pfam03813, Nrap, Nrap protein. Members of this family are
nucleolar RNA-associated proteins (Nrap) which are
highly conserved from yeast (Saccharomyces cerevisiae)
to human. In the mouse, Nrap is ubiquitously expressed
and is specifically localised in the nucleolus. Nrap is
a large nucleolar protein (of more than 1000 amino
acids). Nrap appears to be associated with ribosome
biogenesis by interacting with pre-rRNA primary
transcript.
Length = 929
Score = 27.6 bits (62), Expect = 4.0
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 125 LNTSIINRGKALNSAMSSLQNFDKSIDNFLA 155
L +N K L ++SS Q F K+ FLA
Sbjct: 200 LQGGGLNGNKILLKSLSSYQLF-KATIQFLA 229
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 27.7 bits (62), Expect = 5.1
Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 8/96 (8%)
Query: 98 KLISVYQHDDTTRVKKITEQVNQRYNNLNTSIINRGKALNSAMSSLQNF------DKSID 151
+L + Y ++ +K+ T +++Q +L ++ A +L++ D +
Sbjct: 551 QLNNSYDLNELLDIKQYTPEIDQELESLKVNLSTITLLTPEARRNLEDLASSGLDDINFS 610
Query: 152 NFLAWLSEA--ESTMECVEVETDRQAEKQSTPLLKV 185
NFL + + E + E D A LKV
Sbjct: 611 NFLKQIQKPLTEVNLNSFAEELDALANNLPNGKLKV 646
>gnl|CDD|130785 TIGR01724, hmd_rel, H2-forming
N(5),N(10)-methenyltetrahydromethanopterin
dehydrogenase-related protein. This model represents a
sister clade to the authenticated coenzyme
F420-dependent
N(5),N(10)-methenyltetrahydromethanopterin reductase
(HMD) of TIGR01723. Two members, designated HmdII and
HmdIII, are found. Members are restricted to
methanogens, but the function is unknown [Unknown
function, Enzymes of unknown specificity].
Length = 341
Score = 27.2 bits (60), Expect = 5.1
Identities = 7/36 (19%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 126 NTSIINRGKALNSAMSSLQNFDKSIDNFLAWLSEAE 161
+ +++R + L++A+ + + D + + W+ AE
Sbjct: 271 SMHLLDRQEDLDAALKIISDLDDDV---MKWIEGAE 303
>gnl|CDD|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication,
recombination, and repair].
Length = 440
Score = 27.2 bits (61), Expect = 5.9
Identities = 15/103 (14%), Positives = 43/103 (41%), Gaps = 10/103 (9%)
Query: 35 QRYDAKRQEVDGWLTRMENRMQRMNPVGYTADVLEVQLREQKSIHADLHQFKQQIVLFNQ 94
+ ++Q +D R+ ++ A + R + ++ + + +Q++ Q
Sbjct: 306 RLLSEQQQRLDELAIRLRRALENQ-----LALKKQRLERLTQRLNPQIQRQQQRLQ---Q 357
Query: 95 LTQKLISVYQHDDTTRVKKITEQVNQRYNNLN-TSIINRGKAL 136
L ++L + + +++ V Q +L+ + + RG A+
Sbjct: 358 LERRLDKALRRQLKRKRERLEALVEQ-LESLSPLATLARGYAV 399
>gnl|CDD|220315 pfam09614, Cas_Csy2, CRISPR-associated protein (Cas_Csy2). CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) is a widespread family of prokaryotic direct
repeats with spacers of unique sequence between
consecutive repeats. This entry, typified by YPO2464 of
Yersinia pestis, is a CRISPR-associated (Cas) entry
strictly associated with the Ypest subtype of CRISPR/Cas
locus. It is designated Csy2, for CRISPR/Cas Subtype
Ypest protein 2.
Length = 295
Score = 26.9 bits (60), Expect = 6.6
Identities = 13/56 (23%), Positives = 22/56 (39%)
Query: 129 IINRGKALNSAMSSLQNFDKSIDNFLAWLSEAESTMECVEVETDRQAEKQSTPLLK 184
+++R L A+ LQ+ + AWL A + + E D E + K
Sbjct: 166 LLDRSDLLAEALQRLQDANPEATLLDAWLDFAALNHQPLRDEFDESPEWEYVRKPK 221
>gnl|CDD|119352 cd02873, GH18_IDGF, The IDGF's (imaginal disc growth factors) are a
family of growth factors identified in insects that
include at least five members, some of which are encoded
by genes in a tight cluster. The IDGF's have an
eight-stranded alpha/beta barrel fold and are related to
the glycosyl hydrolase family 18 (GH18) chitinases, but
they have an amino acid substitution known to abolish
chitinase catalytic activity. IDGFs may have evolved
from chitinases to gain new functions as growth factors,
interacting with cell surface glycoproteins involved in
growth-promoting processes.
Length = 413
Score = 26.9 bits (60), Expect = 7.4
Identities = 32/104 (30%), Positives = 44/104 (42%), Gaps = 21/104 (20%)
Query: 61 VGYTADVLEVQLREQKSIHADLHQFKQQIVLFNQLTQK------LISVYQHDDTTRVKKI 114
G AD ++ KS++ DL K L +K L+SV DT
Sbjct: 39 AGIDADTYKI-----KSLNEDLDLDKSHYRAITSLKRKYPHLKVLLSVGGDRDTDE---- 89
Query: 115 TEQVNQRYNNLNTSIINRGKALNSAMSSLQ--NFDKSIDNFLAW 156
E N++Y L S +R +NSA S L+ FD +D LAW
Sbjct: 90 -EGENEKYLLLLESSESRNAFINSAHSLLKTYGFD-GLD--LAW 129
>gnl|CDD|224003 COG1077, MreB, Actin-like ATPase involved in cell morphogenesis
[Cell division and chromosome partitioning].
Length = 342
Score = 26.8 bits (60), Expect = 7.7
Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 15/56 (26%)
Query: 129 IINRGKALNSAMSSLQNFDKSIDNFLAWLSE--------AESTMECVEVETDRQAE 176
I+ RG L + L+ D+ LSE A+ + CV T + E
Sbjct: 282 IVERGIVLTGGGALLRGLDR-------LLSEETGVPVIIADDPLTCVAKGTGKALE 330
>gnl|CDD|222981 PHA03096, PHA03096, p28-like protein; Provisional.
Length = 284
Score = 26.7 bits (59), Expect = 8.9
Identities = 15/67 (22%), Positives = 25/67 (37%)
Query: 107 DTTRVKKITEQVNQRYNNLNTSIINRGKALNSAMSSLQNFDKSIDNFLAWLSEAESTMEC 166
T + K TE N+R N + I + L + + S D D L + +
Sbjct: 217 MTESLYKETEPENRRLNTVIVFIEKINEDLKNNIPSRYWIDDKYDKNLLSFRYKKMHIRK 276
Query: 167 VEVETDR 173
V +E +
Sbjct: 277 VCIELYK 283
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
0.315 0.127 0.352
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,778,162
Number of extensions: 753538
Number of successful extensions: 894
Number of sequences better than 10.0: 1
Number of HSP's gapped: 881
Number of HSP's successfully gapped: 66
Length of query: 186
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 95
Effective length of database: 6,901,388
Effective search space: 655631860
Effective search space used: 655631860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.4 bits)