RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2540
(58 letters)
>gnl|CDD|238091 cd00160, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous
(DH) domain. It appears that PH domains invariably occur
C-terminal to RhoGEF/DH domains.
Length = 181
Score = 50.8 bits (122), Expect = 9e-10
Identities = 21/47 (44%), Positives = 28/47 (59%)
Query: 11 ITVPVQRVTKYPLLLARLYKVTPDHHTGKDLLIEAQHNIQLHLEHIN 57
+ PVQR+TKYPLLL L K TPD H ++ L +A I+ +N
Sbjct: 135 LLKPVQRLTKYPLLLKELLKHTPDGHEDREDLKKALEAIKEVASQVN 181
>gnl|CDD|216028 pfam00621, RhoGEF, RhoGEF domain. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that pfam00169
domains invariably occur C-terminal to RhoGEF/DH
domains.
Length = 179
Score = 49.9 bits (120), Expect = 2e-09
Identities = 19/44 (43%), Positives = 24/44 (54%)
Query: 14 PVQRVTKYPLLLARLYKVTPDHHTGKDLLIEAQHNIQLHLEHIN 57
PVQR+ +YPLLL L K TP H + L +A I+ IN
Sbjct: 135 PVQRIPRYPLLLKELLKHTPPDHPDYEDLKKALEAIKEVASQIN 178
>gnl|CDD|214619 smart00325, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that PH domains
invariably occur C-terminal to RhoGEF/DH domains.
Improved coverage.
Length = 180
Score = 48.5 bits (116), Expect = 6e-09
Identities = 20/47 (42%), Positives = 28/47 (59%)
Query: 11 ITVPVQRVTKYPLLLARLYKVTPDHHTGKDLLIEAQHNIQLHLEHIN 57
+ PVQR+TKYPLLL L K TP+ H ++ L +A I+ +N
Sbjct: 133 LLKPVQRLTKYPLLLKELLKHTPEDHEDREDLKKALKAIKELANQVN 179
>gnl|CDD|132028 TIGR02983, SigE-fam_strep, RNA polymerase sigma-70 factor,
sigma-E family. This group of similar sigma-70 factors
includes the sigE factor from Streptomyces coelicolor.
The family appears to include a paralagous expansion in
the Streptomycetes lineage, while related
Actinomycetales have at most two representatives.
Length = 162
Score = 28.1 bits (63), Expect = 0.18
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 18 VTKYPLLLARLYKVTPDHHTGKDLLIEA 45
+YP LL Y +T D H +DL+ EA
Sbjct: 13 AARYPRLLRTAYLLTGDPHEAEDLVQEA 40
>gnl|CDD|222956 PHA02992, PHA02992, hypothetical protein; Provisional.
Length = 728
Score = 25.8 bits (57), Expect = 1.2
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 27 RLYKVTPDHHTGKDLL--IEAQHNIQLHLEHIN 57
+LY P H DL+ I Q N++L+ HIN
Sbjct: 59 KLYLFKPKHVLFIDLISVITKQKNVELYASHIN 91
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 24.5 bits (53), Expect = 3.8
Identities = 14/54 (25%), Positives = 25/54 (46%)
Query: 4 KLFAQVSITVPVQRVTKYPLLLARLYKVTPDHHTGKDLLIEAQHNIQLHLEHIN 57
KL +T P R+ +YPLLL + K T + + + + ++ L +N
Sbjct: 616 KLELDGYLTKPTTRLARYPLLLEEVLKFTDPDNPDTEDIPKVIDMLREFLSRLN 669
>gnl|CDD|234069 TIGR02950, SigM_subfam, RNA polymerase sigma factor, SigM family.
This family of RNA polymerase sigma factors is a
member of the Sigma-70 subfamily (TIGR02937) and is
restricted to certain lineages of the order Bacillales.
This family encompasses at least two distinct sigma
factors as two proteins are found in each of B.
anthracis, B. subtilis subsp. subtilis str. 168, and B.
lichiniformis (although these are not apparently the
same two in each). One of these is designated as SigM
in B. subtilis (Swiss_Prot: SIGM_BACSU) and is
activated by various stressors.
Length = 154
Score = 23.6 bits (51), Expect = 6.9
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 21 YPLLLARLYKVTPDHHTGKDLLIEAQHNIQLHLEHI 56
+ LY++T D H +DLL E +HL
Sbjct: 5 MHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSF 40
>gnl|CDD|170033 PRK09644, PRK09644, RNA polymerase sigma factor SigM;
Provisional.
Length = 165
Score = 23.3 bits (50), Expect = 8.1
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 28 LYKVTPDHHTGKDLLIEAQHNIQLHLE 54
L+ +T HH +DLL E + ++LE
Sbjct: 18 LFSLTKSHHAAEDLLQETFYRAYIYLE 44
>gnl|CDD|206533 pfam14365, DUF4409, Domain of unknown function (DUF4409).
Length = 117
Score = 23.4 bits (51), Expect = 8.2
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 12 TVPVQRVTKYPLLLARLYK 30
TVP++R TK LL A K
Sbjct: 67 TVPIRRTTKEDLLRASSVK 85
>gnl|CDD|218234 pfam04733, Coatomer_E, Coatomer epsilon subunit. This family
represents the epsilon subunit of the coatomer complex,
which is involved in the regulation of intracellular
protein trafficking between the endoplasmic reticulum
and the Golgi complex.
Length = 288
Score = 23.2 bits (50), Expect = 9.6
Identities = 12/39 (30%), Positives = 15/39 (38%), Gaps = 2/39 (5%)
Query: 20 KYPLLLARLYKVTPDHHTGKDLLIEAQHNIQLHLEHINS 58
K P L L V H GK + ++ QL L H
Sbjct: 231 KDPETLINL--VVCALHLGKPAEVSNRNLSQLKLSHPTH 267
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
0.323 0.136 0.387
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,879,046
Number of extensions: 194693
Number of successful extensions: 167
Number of sequences better than 10.0: 1
Number of HSP's gapped: 167
Number of HSP's successfully gapped: 10
Length of query: 58
Length of database: 10,937,602
Length adjustment: 30
Effective length of query: 28
Effective length of database: 9,606,982
Effective search space: 268995496
Effective search space used: 268995496
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 (22.0 bits)
S2: 53 (24.2 bits)