RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15889
(92 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 38.6 bits (91), Expect = 1e-05
Identities = 10/15 (66%), Positives = 15/15 (100%)
Query: 10 RVRVWFKNRRAKWRK 24
+V+VWF+NRRAKW++
Sbjct: 43 QVKVWFQNRRAKWKR 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 = 36.5 bits (85), Expect = 1e-04
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 10 RVRVWFKNRRAKWRKRE 26
+V++WF+NRRAK ++ E
Sbjct: 43 QVKIWFQNRRAKLKRSE 59
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 34.1 bits (79), Expect = 8e-04
Identities = 10/14 (71%), Positives = 14/14 (100%)
Query: 10 RVRVWFKNRRAKWR 23
+V+VWF+NRRAKW+
Sbjct: 44 QVKVWFQNRRAKWK 57
>gnl|CDD|149722 pfam08750, CNP1, CNP1-like family. This family of proteins are
likely to be lipoproteins. CNP1 (cryptic neisserial
protein) has been expressed in E. coli and shown to be
localised periplasmicly.
Length = 139
Score = 27.6 bits (62), Expect = 0.68
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 14 WFKNRRAKWRKRERNAMNAAAAA 36
W + RRA+W++ E A N AA
Sbjct: 92 WSRARRAEWQRIEDGAPNRYHAA 114
>gnl|CDD|201972 pfam01783, Ribosomal_L32p, Ribosomal L32p protein family.
Length = 56
Score = 26.1 bits (58), Expect = 0.99
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 16 KNRRAKWRKRERNAMNAAAAAAV 38
K + +K RKR+R A A +
Sbjct: 4 KRKTSKSRKRKRRAHWKLKAPNL 26
>gnl|CDD|239650 cd03678, MM_CoA_mutase_1, Coenzyme B12-dependent-methylmalonyl
coenzyme A (CoA) mutase (MCM) family, unknown subfamily
1; composed of uncharacterized bacterial proteins
containing a C-terminal MCM domain. MCM catalyzes the
isomerization of methylmalonyl-CoA to succinyl-CoA. The
reaction proceeds via radical intermediates beginning
with a substrate-induced homolytic cleavage of the Co-C
bond of coenzyme B12 to produce cob(II)alamin and the
deoxyadenosyl radical. MCM plays an important role in
the conversion of propionyl-CoA to succinyl-CoA during
the degradation of propionate for the Krebs cycle. In
some bacteria, MCM is involved in the reverse metabolic
reaction, the rearrangement of succinyl-CoA to
methylmalonyl-CoA. Members of this subfamily also
contain an N-terminal coenzyme B12 binding domain
followed by a domain similar to the E. coli ArgK
membrane ATPase.
Length = 495
Score = 27.5 bits (61), Expect = 1.0
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 12 RVWFKNRRAKWRKRERNAM---------NAAAAAAVDFKNGFSTQFNGLMQTFPDTDSLY 62
R+W + R K+ ER+ M + A +DF N T L + + +SL+
Sbjct: 320 RIWARAMREKYGANERSQMLKYHIQTSGRSLHAQEIDF-NDIRTTLQALYAIYDNCNSLH 378
Query: 63 TSAY 66
T+AY
Sbjct: 379 TNAY 382
>gnl|CDD|237038 PRK12286, rpmF, 50S ribosomal protein L32; Reviewed.
Length = 57
Score = 26.0 bits (58), Expect = 1.1
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 16 KNRRAKWRKRERNAMNAAAAAAV 38
K + +K RKR+R A A +
Sbjct: 5 KRKTSKSRKRKRRAHFKLKAPGL 27
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 26.6 bits (59), Expect = 1.4
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 11 VRVWFKNRRAKWRK 24
V++WF+N+RAK +K
Sbjct: 95 VQIWFQNKRAKEKK 108
>gnl|CDD|221193 pfam11735, CAP59_mtransfer, Cryptococcal mannosyltransferase 1.
The capsule of pathogenic fungi is a complex
polysaccharide whose formation is determined by a number
of enzymes including, most importantly,
alpha-1,3-mannosyltransferase 1, EC:2.4.1.-.
Length = 244
Score = 26.4 bits (59), Expect = 1.8
Identities = 12/32 (37%), Positives = 13/32 (40%), Gaps = 9/32 (28%)
Query: 27 RNAMNAAAAAAVDFKNGFSTQFNGLMQTFPDT 58
N N AAA A+DF N F DT
Sbjct: 137 TNVGNYAAACAMDFSNPP---------KFYDT 159
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 26.4 bits (58), Expect = 2.1
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 67 SSYNNWASKVPSPLGT-IGVNDL 88
S+Y NWA VPS T IG D+
Sbjct: 202 SAYYNWAISVPSMKKTGIGFKDI 224
>gnl|CDD|216060 pfam00686, CBM_20, Starch binding domain.
Length = 96
Score = 25.7 bits (57), Expect = 2.3
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 60 SLYTSAYSSYNNWASKVPSPLGT 82
L S YSSY W+ V P GT
Sbjct: 37 KLSASQYSSYPLWSGTVSLPAGT 59
>gnl|CDD|237578 PRK13983, PRK13983, diaminopimelate aminotransferase; Provisional.
Length = 400
Score = 26.0 bits (58), Expect = 3.1
Identities = 20/63 (31%), Positives = 26/63 (41%), Gaps = 7/63 (11%)
Query: 7 LWLRVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPDTDSLYTSAY 66
LWL+ V K A N +NA AAA DF L + F D L+ Y
Sbjct: 197 LWLKFTVKGKQCHAS---TPENGINAHRAAA-DFALELD---EALHEKFNAKDPLFDPPY 249
Query: 67 SSY 69
S++
Sbjct: 250 STF 252
>gnl|CDD|223844 COG0773, MurC, UDP-N-acetylmuramate-alanine ligase [Cell envelope
biogenesis, outer membrane].
Length = 459
Score = 25.6 bits (57), Expect = 4.4
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 28 NAMNAAAAAAVDFKNGFS 45
N +NA AA AV + G
Sbjct: 281 NVLNALAAIAVARELGID 298
>gnl|CDD|211326 cd02552, PseudoU_synth_TruD_like, Pseudouridine synthase, TruD
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruD and Saccharomyces cerevisiae Pus7.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). E. coli TruD and S. cerevisiae
Pus7 make psi13 in cytoplasmic tRNAs. In addition S.
cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2
snRNA) and psi35 in pre-tRNATyr. Psi35 in U2 snRNA and
psi13 in tRNAs are highly phylogenetically conserved.
Psi34 is the mammalian U2 snRNA counterpart of yeast U2
snRNA psi35.
Length = 232
Score = 25.2 bits (56), Expect = 4.5
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 5/26 (19%)
Query: 52 MQTFPDTDSLYTSAYSSY--NNWASK 75
+Q F S+Y AY SY N S+
Sbjct: 153 LQRFG---SMYLHAYQSYLFNEVLSE 175
>gnl|CDD|172773 PRK14285, PRK14285, chaperone protein DnaJ; Provisional.
Length = 365
Score = 25.3 bits (55), Expect = 5.3
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 17 NRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPDTDSLYTSAYS 67
N+RA++ + A GFS F+G F D ++ S ++
Sbjct: 60 NKRAQYDRFGHTAFEGGGGF-----EGFSGGFSGFSDIFEDFGDIFDSFFT 105
>gnl|CDD|181325 PRK08252, PRK08252, enoyl-CoA hydratase; Provisional.
Length = 254
Score = 25.0 bits (55), Expect = 6.8
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 4/21 (19%)
Query: 23 RKRERNAMNAAA----AAAVD 39
R RNA+NAA AAA+D
Sbjct: 20 RPEARNAVNAAVAQGLAAALD 40
>gnl|CDD|236433 PRK09259, PRK09259, putative oxalyl-CoA decarboxylase; Validated.
Length = 569
Score = 24.9 bits (55), Expect = 7.3
Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 6/24 (25%)
Query: 24 KRERNAMNAAAAAAVDFKNGFSTQ 47
+ E++A NAAAAA GF TQ
Sbjct: 54 RHEQSAGNAAAAA------GFLTQ 71
>gnl|CDD|169983 PRK09579, PRK09579, multidrug efflux protein; Reviewed.
Length = 1017
Score = 24.8 bits (54), Expect = 8.4
Identities = 8/36 (22%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 31 NAAAAAAVDFKNGFSTQFNGLMQTFPDTDSLYTSAY 66
++ A +D+ N ++ +F + ++FP+ Y S++
Sbjct: 563 SSPQPANLDYLNAYTDEFTPIFKSFPE----YYSSF 594
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
0.319 0.129 0.408
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,757,342
Number of extensions: 368242
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 425
Number of HSP's successfully gapped: 29
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
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 (21.8 bits)
S2: 53 (24.1 bits)