RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12411
(161 letters)
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 44.8 bits (106), Expect = 5e-06
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 114 ASKQKKELSKVDHSTIEYLPFRKDFYVEVPEIARMTPEEVEK 155
+S K L +D +I +PF K+FY E PE++ ++ +EV++
Sbjct: 69 SSTLGKRLQPIDWKSINLVPFEKNFYKEHPEVSALSSKEVDE 110
>gnl|CDD|131051 TIGR01996, PTS-II-BC-sucr, PTS system, sucrose-specific IIBC
component. This model represents the fused enzyme II B
and C components of the sucrose-specific PTS sugar
transporter system. Sucrose is converted to
sucrose-6-phosphate in the process of translocation into
the cell. Some of these transporters lack their own IIA
domains and instead use the glucose IIA protein (IIAglc
or Crr). The exceptions to this rule are Staphylococci,
Streptococci, Lactococci, Lactobacilli, etc. which
contain their own A domain as a C-terminal fusion. This
family is closely related to the trehalose transporting
PTS IIBC enzymes and the B and C domains of each are
described by subfamily-domain level TIGRFAMs models
(TIGR00826 and TIGR00852, respectively).
Length = 461
Score = 30.7 bits (70), Expect = 0.29
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 45 KVNKPAVPTTADVKPADSGSKPAGVVIVTGVVKKSVEKAKGELMEENQDGLEYSSEEEQE 104
K++K A+ VK S ++I TGVV K V + + GL SS EQ+
Sbjct: 38 KIDKKAIENLDGVKGTFFNSGQYQIIIGTGVVNK-VYDE----IVK-LTGLSESSTSEQK 91
Query: 105 DLTSTAANLASKQKKELSKV 124
+ N + + LS +
Sbjct: 92 AEAAKKMNPFQRFARTLSDI 111
>gnl|CDD|180626 PRK06565, PRK06565, amidase; Validated.
Length = 566
Score = 29.7 bits (67), Expect = 0.58
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 14/76 (18%)
Query: 5 NLEDD--SDEDENDNKDENGKTAEEDIDPLDAFMQGVHEEMRKVNKP---------AV-- 51
N E D + DE N + G + + I L ++G+ E+ RK++ AV
Sbjct: 414 NREGDLAAGMDEYVNMAKRGLKSWDQIPTLPDGLRGL-EKTRKLDLEDWMDGLGLDAVLF 472
Query: 52 PTTADVKPADSGSKPA 67
PT ADV PAD+ PA
Sbjct: 473 PTVADVGPADADVNPA 488
>gnl|CDD|212661 cd07777, FGGY_SHK_like, sedoheptulokinase-like proteins; a
subfamily of the FGGY family of carbohydrate kinases.
This subfamily is predominantly composed of
uncharacterized bacterial and eukaryotic proteins with
similarity to human sedoheptulokinase (SHK, also known
as D-altro-heptulose or heptulokinase, EC 2.7.1.14)
encoded by the carbohydrate kinase-like (CARKL/SHPK)
gene. SHK catalyzes the ATP-dependent phosphorylation of
sedoheptulose to produce sedoheptulose 7-phosphate and
ADP. The presence of Mg2+ or Mn2+ might be required for
catalytic activity. Members of this subfamily belong to
the FGGY family of carbohydrate kinases, the monomers of
which contain two large domains, which are separated by
a deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 448
Score = 29.2 bits (66), Expect = 0.90
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 108 STAANLASKQKKELSKVDHSTIEYLPFRKDFYVEV 142
T+A L+ + V ++ EY P+ K+ Y+ V
Sbjct: 263 GTSAQLSFLPVFKPETVPPASPEYRPYFKNHYLAV 297
>gnl|CDD|119401 cd06662, SURF1, SURF1 superfamily. Surf1/Shy1 has been implicated
in the posttranslational steps of the biogenesis of the
mitochondrially-encoded Cox1 subunit of cytochrome c
oxidase (complex IV). Cytochrome c oxidase (complex IV),
the terminal electron-transferring complex of the
respiratory chain, is an assemblage of nuclear and
mitochondrially-encoded subunits. Its assembly is
mediated by nuclear encoded assembly factors, one of
which is Surf1/Shy1. Mutations in human Surf1 are a
major cause of Leigh syndrome, a severe
neurodegenerative disorder.
Length = 202
Score = 28.5 bits (64), Expect = 1.4
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 1/44 (2%)
Query: 51 VPTTADVKPADSGSKPAGVVIVTGVVKKSVEKAKGELMEENQDG 94
VP AD + + P G V VTG ++ E L +
Sbjct: 95 VPADADRPALPAVAPPTGEVTVTGRLRPP-EPRGLFLPPNDPAA 137
>gnl|CDD|217310 pfam02993, MCPVI, Minor capsid protein VI. This minor capsid
protein may act as a link between the external capsid
and the internal DNA-protein core. The C-terminal 11
residues may function as a protease cofactor leading to
enzyme activation.
Length = 238
Score = 28.2 bits (63), Expect = 1.6
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 1/57 (1%)
Query: 25 AEEDIDPLDAFMQGVHEEM-RKVNKPAVPTTADVKPADSGSKPAGVVIVTGVVKKSV 80
EE I P A ++ + M V P T ++ PA P T VV +
Sbjct: 151 YEETIKPGPAPVEEPVDSMAIAVPAIDTPVTLELPPAPQPPPPVVPQPSTMVVHRRS 207
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 27.9 bits (62), Expect = 3.3
Identities = 15/70 (21%), Positives = 34/70 (48%), Gaps = 7/70 (10%)
Query: 85 GELMEENQDGLEYSSEEEQEDLTSTAANLASKQKKELSKVDHSTIEYLPFRKDFYVEVPE 144
E EE+ D L +++L + L +++ + + +++Y+P +F ++ +
Sbjct: 143 KEAREEDADDL-------RDELAADLEELDAERDRLIEATRRLSVDYVPEDDEFVDDIGD 195
Query: 145 IARMTPEEVE 154
R+T EEV
Sbjct: 196 DERLTAEEVR 205
>gnl|CDD|173241 PRK14780, PRK14780, lipoprotein signal peptidase; Provisional.
Length = 263
Score = 27.2 bits (60), Expect = 4.0
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 1 MKKWNLEDDSDEDENDNKDENGKTAEEDID 30
+ KW + DS++++ DEN E +
Sbjct: 223 IIKWKKDKDSEDNKKKIADENDLEINEPSN 252
>gnl|CDD|234101 TIGR03074, PQQ_membr_DH, membrane-bound PQQ-dependent
dehydrogenase, glucose/quinate/shikimate family. This
protein family has a phylogenetic distribution very
similar to that coenzyme PQQ biosynthesis enzymes, as
shown by partial phylogenetic profiling. Members of this
family have several predicted transmembrane helices in
the N-terminal region, and include the quinoprotein
glucose dehydrogenase (EC 1.1.5.2) of Escherichia coli
and the quinate/shikimate dehydrogenase of Acinetobacter
sp. ADP1 (EC 1.1.99.25). Sequences closely related
except for the absense of the N-terminal hydrophobic
region, scoring in the gray zone between the trusted and
noise cutoffs, include PQQ-dependent glycerol (EC
1.1.99.22) and and other polyol (sugar alcohol)
dehydrogenases.
Length = 764
Score = 27.3 bits (61), Expect = 4.1
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 37 QGVHEEMRKVNKPAVPTTADVKPADSGSKPAGVVIVT 73
Q VH ++ ++ PA P+ D+ AD + PA +V T
Sbjct: 431 QTVHHDLWDMDVPAQPSLVDLPDADGTTVPA-LVAPT 466
>gnl|CDD|100027 cd00396, PurM-like, AIR (aminoimidazole ribonucleotide) synthase
related protein. This family includes Hydrogen
expression/formation protein HypE, AIR synthases, FGAM
(formylglycinamidine ribonucleotide) synthase and
Selenophosphate synthetase (SelD). The N-terminal domain
of AIR synthase forms the dimer interface of the
protein, and is suggested as a putative ATP binding
domain.
Length = 222
Score = 27.0 bits (60), Expect = 5.0
Identities = 16/53 (30%), Positives = 24/53 (45%)
Query: 28 DIDPLDAFMQGVHEEMRKVNKPAVPTTADVKPADSGSKPAGVVIVTGVVKKSV 80
++D L+ + GV E ++ P V V P G K + V GVV+K
Sbjct: 53 EVDILEDVVDGVAEACNQLGVPIVGGHTSVSPGTMGHKLSLAVFAIGVVEKDR 105
>gnl|CDD|144440 pfam00845, Gemini_BL1, Geminivirus BL1 movement protein.
Geminiviruses encode two movement proteins that are
essential for systemic infection of their host but
dispensable for replication and encapsidation.
Length = 276
Score = 26.5 bits (59), Expect = 6.5
Identities = 18/50 (36%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 108 STAANLASKQKKELSKVDHSTIEY---LPFRKDFYVEVPEI--ARMTPEE 152
STA S+ K+DH IEY +P V V EI R+T E
Sbjct: 25 STAEQKTSRLSGRCMKIDHCVIEYRNQVPINATGSVIV-EIHDKRLTDNE 73
>gnl|CDD|149105 pfam07851, TMPIT, TMPIT-like protein. A number of members of this
family are annotated as being transmembrane proteins
induced by tumour necrosis factor alpha, but no
literature was found to support this.
Length = 330
Score = 26.6 bits (59), Expect = 6.6
Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 13/61 (21%)
Query: 101 EEQEDLTSTAANLASKQKKELSKVDHSTIEYLPFRKDFYVEVPEIARMTPEEVEKYKEVD 160
EE E L + ++Q+K L ++ S + +TPE+ E ++++
Sbjct: 28 EEVEKLQEQCTSAIARQRKRLKQLIVSLKKLKK-------------SLTPEDSELVEQLE 74
Query: 161 N 161
Sbjct: 75 E 75
>gnl|CDD|216402 pfam01268, FTHFS, Formate--tetrahydrofolate ligase.
Length = 557
Score = 26.6 bits (60), Expect = 6.6
Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 56 DVKPADSGSKPAGVVIVTGV--VKKSVEKAKGELMEENQDGLE 96
D+K SG KP VV+V V +K AK +L EEN + LE
Sbjct: 312 DIKCRKSGLKPDAVVLVATVRALKMHGGVAKDDLTEENLEALE 354
>gnl|CDD|188896 cd09497, SAM_caskin1,2_repeat1, SAM domain of caskin protein repeat
1. SAM (sterile alpha motif) domain repeat 1 of
caskin1,2 proteins is a protein-protein interaction
domain. Caskin has two tandem SAM domains. Caskin
protein is known to interact with membrane-associated
guanylate kinase CASK, and apparently may play a role in
neural development, synaptic protein targeting, and
regulation of gene expression.
Length = 66
Score = 24.9 bits (55), Expect = 6.8
Identities = 13/24 (54%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 130 EYLP-FRKDFYVEVPEIARMTPEE 152
EY P F K Y ++P I+RMTPE+
Sbjct: 18 EYTPNFIKAGY-DLPTISRMTPED 40
>gnl|CDD|171679 PRK12717, flgL, flagellar hook-associated protein FlgL;
Provisional.
Length = 523
Score = 26.6 bits (59), Expect = 6.9
Identities = 11/26 (42%), Positives = 12/26 (46%)
Query: 50 AVPTTADVKPADSGSKPAGVVIVTGV 75
A P TAD KP SG+ GV
Sbjct: 356 AQPVTADSKPISSGTLTGNTATAAGV 381
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
0.302 0.124 0.332
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,158,033
Number of extensions: 730473
Number of successful extensions: 909
Number of sequences better than 10.0: 1
Number of HSP's gapped: 885
Number of HSP's successfully gapped: 80
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.8 bits)
S2: 55 (25.1 bits)