RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4078
(269 letters)
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 73.8 bits (182), Expect = 2e-17
Identities = 22/57 (38%), Positives = 30/57 (52%)
Query: 82 PTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138
R RT +QL L + NP P +E+L + LS R ++VWFQN+R K K
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 73.8 bits (182), Expect = 2e-17
Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
R RT +QL L + NP P +E+L + L+ R +++WFQN+R K K+
Sbjct: 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 70.6 bits (174), Expect = 4e-16
Identities = 21/56 (37%), Positives = 31/56 (55%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT +QL L + N P A +E+L + L+ R ++VWFQN+R K K+
Sbjct: 2 RKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 55.9 bits (135), Expect = 8e-10
Identities = 25/94 (26%), Positives = 45/94 (47%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
G P R ++QL L + NP P ++ + +L + N+ P+ +++WFQNKR
Sbjct: 45 QDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRA 104
Query: 136 KDKKRALAMKQQLQQEKDGRKMGYGSMQGIPMVA 169
K+KK+ +Q E++ GS+ +
Sbjct: 105 KEKKKRSGKVEQRPGEEEADLAKIGSLSTGQISI 138
>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain. This is a homeobox
transcription factor KN domain conserved from fungi to
human and plants.
Length = 40
Score = 33.6 bits (78), Expect = 0.005
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 104 NPRPDALMKEQLVEMTNLSPRVIRVWFQNKR 134
NP P K +L T LS + I WF N R
Sbjct: 8 NPYPSEEEKSELARQTGLSRKQIDNWFINAR 38
>gnl|CDD|224877 COG1966, CstA, Carbon starvation protein, predicted membrane
protein [Signal transduction mechanisms].
Length = 575
Score = 32.3 bits (74), Expect = 0.28
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 144 MKQQLQQEKDGRKMGYGSMQGIPMVA 169
+QL+ E D R +GYG+M G +A
Sbjct: 318 TAKQLENESDARFIGYGAMLGEGFLA 343
>gnl|CDD|217102 pfam02554, CstA, Carbon starvation protein CstA. This family
consists of Carbon starvation protein CstA a predicted
membrane protein. It has been suggested that CstA is
involved in peptide utilisation.
Length = 382
Score = 31.0 bits (71), Expect = 0.67
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 147 QLQQEKDGRKMGYGSM 162
QL E D R +GYG+M
Sbjct: 321 QLDNESDARFVGYGAM 336
>gnl|CDD|202093 pfam02023, SCAN, SCAN domain. The SCAN domain (named after
SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in
several pfam00096 proteins. The domain has been shown to
be able to mediate homo- and hetero-oligomerisation.
Length = 93
Score = 29.1 bits (66), Expect = 0.79
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 106 RPDALMKEQLVEMTNLS------PRVIRVWFQNKRCKDKKRALAMKQQLQQEKDGRK 156
RP+ KEQ++E+ L P ++ W Q + + A+A+ + L +E D
Sbjct: 37 RPEIHTKEQILELLVLEQFLTILPEELQAWVQEHHPESGEEAVALVEDLTRELDEPG 93
>gnl|CDD|146900 pfam04492, Phage_rep_O, Bacteriophage replication protein O.
Replication protein O is necessary for the initiation of
bacteriophage DNA replication. Protein O interacts with
the lambda replication origin, and also with replication
protein P to form an oligomer. It is speculated that the
N-terminal half interacts with the replication origin
while the C terminal half mediates protein-protein
interaction.
Length = 100
Score = 28.9 bits (65), Expect = 0.88
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 11/62 (17%)
Query: 97 LRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQLQQEKDGRK 156
+R Y N D + EQ+ E+T LS + K++L + + Q DGR+
Sbjct: 42 IRKTYGWNKPMDRVTNEQIAELTGLSR---------THVSEAKKSLVKRGIIIQ--DGRQ 90
Query: 157 MG 158
+G
Sbjct: 91 IG 92
>gnl|CDD|183859 PRK13103, secA, preprotein translocase subunit SecA; Reviewed.
Length = 913
Score = 28.8 bits (64), Expect = 3.5
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 131 QNKRCKDKKRALAMKQQLQQEK----DGRKMGYGSMQGIPMVASSPVRHDSPIGMNAL 184
+ R + + LA + Q Q + + ++G + VAS+PVR++ +G N
Sbjct: 839 EEARLRREAEELASRMQFQHAEAPGLEQPQLGEEEEEPAVAVASAPVRNEQKLGRNEP 896
>gnl|CDD|223333 COG0255, RpmC, Ribosomal protein L29 [Translation, ribosomal
structure and biogenesis].
Length = 69
Score = 26.5 bits (59), Expect = 4.2
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 15/52 (28%)
Query: 58 KEQLVEMTN-----LFLGRVRKVSGGDGKPTRVR----------TVLNEKQL 94
E+L E LF R + +G P R+R TVL EK+L
Sbjct: 13 VEELEEELRELKKELFNLRFQLATGQLENPHRIREVRRDIARILTVLREKEL 64
>gnl|CDD|165252 PHA02942, PHA02942, putative transposase; Provisional.
Length = 383
Score = 28.1 bits (62), Expect = 5.0
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 120 NLSPRVIRVWFQNKRCKDKKRALAMKQQLQQEKDGRKMG 158
NL + R W +NKR + R+ K +L E RK+G
Sbjct: 217 NLQKKYPRRWKENKRILHRARSFHHKAKLIMEDFARKVG 255
>gnl|CDD|128708 smart00431, SCAN, leucine rich region.
Length = 113
Score = 26.9 bits (60), Expect = 5.1
Identities = 13/57 (22%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 106 RPDALMKEQLVEMTNLS------PRVIRVWFQNKRCKDKKRALAMKQQLQQEKDGRK 156
RP+ KEQ++E+ L P ++ W + + + A+ + + L++E D
Sbjct: 35 RPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLLEDLERELDEPG 91
>gnl|CDD|163028 TIGR02812, fadR_gamma, fatty acid metabolism transcriptional
regulator FadR. Members of this family are FadR, a
transcriptional regulator of fatty acid metabolism,
including both biosynthesis and beta-oxidation. It is
found exclusively in a subset of Gammaproteobacteria,
with strictly one copy per genome. It has an N-terminal
DNA-binding domain and a less well conserved C-terminal
long chain acyl-CoA-binding domain. FadR from this
family heterologously expressed in Escherichia coli show
differences in regulatory response and fatty acid
binding profiles. The family is nevertheless designated
equivalog, as all member proteins have at least
nominally the same function [Fatty acid and phospholipid
metabolism, Biosynthesis, Fatty acid and phospholipid
metabolism, Degradation, Regulatory functions, DNA
interactions].
Length = 235
Score = 27.3 bits (61), Expect = 7.6
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEM-TNLSPRVIRVWFQNKRCKDK 138
GKPT+V L+ L T + + + L+ TN+S IR F+N +
Sbjct: 65 GKPTKVNNFWETSGLNILETLIRLDGESVPSLIDNLLSARTNISAIYIRYAFKN----NP 120
Query: 139 KRALAMKQQLQQEKD 153
++AL + + +D
Sbjct: 121 EKALEVLANANELED 135
>gnl|CDD|212523 cd09999, Arginase-like_1, Arginase-like amidino hydrolase family.
This family includes arginase, also known as
arginase-like amidino hydrolase family, as well as
arginase-like proteins and are found in bacteria,
archaea and eykaryotes, but does not include metazoan
arginases. Arginase is a binuclear Mn-dependent
metalloenzyme and catalyzes hydrolysis of L-arginine to
L-ornithine and urea (Arg, EC 3.5.3.1), the reaction
being the fifth and final step in the urea cycle,
providing the path for the disposal of nitrogenous
compounds. Arginase controls cellular levels of arginine
and ornithine which are involved in protein
biosynthesis, and in production of creatine, polyamines,
proline and nitric acid.
Length = 272
Score = 27.6 bits (62), Expect = 7.6
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 194 KALSDFALHTDLDRLDPSAAP 214
+ LS +H DLD LDP+ P
Sbjct: 197 EGLSGVWIHLDLDVLDPAIFP 217
>gnl|CDD|153421 cd07936, SCAN, SCAN oligomerization domain. The SCAN domain (named
after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is
found in several vertebrate proteins that contain C2H2
zinc finger motifs, many of which may be transcription
factors playing roles in cell survival and
differentiation. This protein-interaction domain is able
to mediate homo- and hetero-oligomerization of
SCAN-containing proteins. Some SCAN-containing proteins,
including those of lower vertebrates, do not contain
zinc finger motifs. It has been noted that the SCAN
domain resembles a domain-swapped version of the
C-terminal domain of the HIV capsid protein. This domain
model features elements common to the three general
groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B).
The SCAND1 protein is truncated at the C-terminus with
respect to this model, the SCAND2 protein appears to
have a truncated central helix.
Length = 85
Score = 25.7 bits (57), Expect = 10.0
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 94 LHTLRTCYNANPRPDALMKEQLVEMTNLS------PRVIRVWFQNKRCKDKKRA 141
L LR RP+ KEQ++E+ L P ++ W + ++ + + A
Sbjct: 23 LQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEA 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
0.313 0.131 0.390
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,631,478
Number of extensions: 1276035
Number of successful extensions: 816
Number of sequences better than 10.0: 1
Number of HSP's gapped: 814
Number of HSP's successfully gapped: 29
Length of query: 269
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 174
Effective length of database: 6,723,972
Effective search space: 1169971128
Effective search space used: 1169971128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.1 bits)