RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13857
(259 letters)
>gnl|CDD|219729 pfam08148, DSHCT, DSHCT (NUC185) domain. This C terminal domain is
found in DOB1/SK12/helY-like DEAD box helicases.
Length = 178
Score = 112 bits (283), Expect = 7e-31
Identities = 42/113 (37%), Positives = 70/113 (61%), Gaps = 4/113 (3%)
Query: 142 INSQGIVQLKGNIACEMGSKNELLITELLFQNKLVNFTPEEIAALLSCLVFQSKT-TTPT 200
I+ G+V LKG +ACE+ S++ELL+TELLF + PEE+AALLS VF+ +
Sbjct: 1 IDDDGVVTLKGRVACEISSEDELLLTELLFSGFFNDLDPEELAALLSAFVFEERRDDEGY 60
Query: 201 ELPESLKQGMSIIADMNIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWA 253
L + ++ + ++ ++ +E++HG++ + E +FGL++VVYEWA
Sbjct: 61 PPSLELAEALNRLLEIARKLAKVEREHGLDEPEYVER---FDFGLMEVVYEWA 110
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 93.2 bits (232), Expect = 2e-21
Identities = 49/160 (30%), Positives = 87/160 (54%), Gaps = 10/160 (6%)
Query: 100 HIYKRKEDHNRLSELKHLLSHKGMSLY--ADYDSKVKVLQELNYINSQGIVQLKGNIACE 157
I + +E++ L S +L DY + +VL++L +I +V +KG +A E
Sbjct: 818 LIENELLLSDLQAEIEDL-SSSIEALSFLDDYKTLQEVLKKLGFIEDNAVVLIKGRVAAE 876
Query: 158 MGSKNELLITELLFQNKLVNFTPEEIAALLSCLVFQSKTTTPT----ELPESLKQGMSII 213
+ S++ELL+TEL+F + + PEE+AALLS VF+ KT T E+ +L+ + +
Sbjct: 877 ISSEDELLLTELIFSGEFNDLEPEELAALLSAFVFEEKTDDGTAEAPEITPALRDALLRL 936
Query: 214 ADMNIEVESIEKKHGVERDKSSEEADNLNFGLVQVVYEWA 253
++ ++ + +E E ++ + GL++VVYEWA
Sbjct: 937 LELARKLNKDQNSSQIE---IYPELNDFSVGLMEVVYEWA 973
>gnl|CDD|143505 cd06836, PLPDE_III_ODC_DapDC_like_1, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Uncharacterized Proteins with
similarity to Ornithine and Diaminopimelate
Decarboxylases. This subfamily contains uncharacterized
proteins with similarity to ornithine decarboxylase
(ODC) and diaminopimelate decarboxylase (DapDC). ODC and
DapDC are fold type III PLP-dependent enzymes that
contain an N-terminal PLP-binding TIM-barrel domain and
a C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. They exist as homodimers with active
sites that lie at the interface between the TIM barrel
domain of one subunit and the beta-sandwich domain of
the other subunit. ODC participates in the formation of
putrescine by catalyzing the decarboxylation of
ornithine, the first step in polyamine biosynthesis.
DapDC participates in the last step of lysine
biosynthesis, the conversion of
meso-2,6-diaminoheptanedioate to L-lysine. Proteins in
this subfamily may function as PLP-dependent
decarboxylases. Homodimer formation and the presence of
the PLP cofactor may be required for catalytic activity.
Length = 379
Score = 40.8 bits (96), Expect = 4e-04
Identities = 26/92 (28%), Positives = 36/92 (39%), Gaps = 23/92 (25%)
Query: 133 VKVLQELNYINSQGIVQLKGNIACEMGSKNELLITELLFQNKLVNFTPEEIAALLSCLVF 192
V VL+ L + E+ S EL + F PE I VF
Sbjct: 40 VPVLRLLA----------EAGAGAEVASPGELELALA------AGFPPERI-------VF 76
Query: 193 QSKTTTPTELPESLKQGMSIIADMNIEVESIE 224
S T EL E+L+ G++I D E+E I+
Sbjct: 77 DSPAKTRAELREALELGVAINIDNFQELERID 108
>gnl|CDD|130855 TIGR01796, CM_mono_aroH, monofunctional chorismate mutase, gram
positive type, clade 1. This model represents a family
of monofunctional (non-fused) chorismate mutases from
gram positive bacteria (Firmicutes) and cyanobacteria.
Trusted members of the family are found in operons with
other enzymes of the chorismate pathways, both up- and
downstream of CM (Listeria, Bacillus, Oceanobacillus) or
are the sole CM in the genome where the other members of
the chorismate pathways are found elsewhere in the
genome (Nostoc, Thermosynechococcus) [Amino acid
biosynthesis, Aromatic amino acid family].
Length = 117
Score = 31.3 bits (71), Expect = 0.15
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 3/42 (7%)
Query: 145 QGIVQLKGNIACEMGSKNELLITELLFQNKLVNFTPEEIAAL 186
+G ++ N A E+G L+TEL+ +N+L TPE++ ++
Sbjct: 5 RGATTVERNEAEEIGEAVAELLTELMERNEL---TPEDLISV 43
>gnl|CDD|239104 cd02424, Peptidase_C39E, A sub-family of peptidase family C39.
Peptidase family C39 mostly contains
bacteriocin-processing endopeptidases from bacteria. The
cysteine peptidases in family C39 cleave the
"double-glycine" leader peptides from the precursors of
various bacteriocins (mostly non-lantibiotic). The
cleavage is mediated by the transporter as part of the
secretion process. Bacteriocins are antibiotic proteins
secreted by some species of bacteria that inhibit the
growth of other bacterial species. The bacteriocin is
synthesized as a precursor with an N-terminal leader
peptide, and processing involves removal of the leader
peptide by cleavage at a Gly-Gly bond, followed by
translocation of the mature bacteriocin across the
cytoplasmic membrane. Most endopeptidases of family C39
are N-terminal domains in larger proteins (ABC
transporters) that serve both functions. The proposed
protease active site is conserved in this sub-family,
which contains Colicin V perocessing peptidase.
Length = 129
Score = 28.8 bits (65), Expect = 1.4
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 98 FYHIYKRKEDHNRLSELKHLLSHKGMSLY 126
+ H YK+K D N L ++K L G+S+Y
Sbjct: 21 YNHYYKKKYDLNEL-KIKANLKKNGLSIY 48
>gnl|CDD|223937 COG1005, NuoH, NADH:ubiquinone oxidoreductase subunit 1 (chain H)
[Energy production and conversion].
Length = 332
Score = 28.8 bits (65), Expect = 2.7
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 59 MLTLLTSDPVML-GSLSMNHTIVNIQVQNIWGVVNTPI 95
L++L VML GSL++ IVN Q +W ++ PI
Sbjct: 161 GLSVLA--VVMLAGSLNLV-DIVNAQSGLLWNILLQPI 195
>gnl|CDD|235458 PRK05427, PRK05427, putative manganese-dependent inorganic
pyrophosphatase; Provisional.
Length = 308
Score = 28.6 bits (65), Expect = 2.9
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 12/48 (25%)
Query: 180 PEEIA-ALLSC-----LVFQSKTTTPT--ELPESLKQGMSIIADMNIE 219
P+EIA +LS L+F+S TTT E L + IA ++IE
Sbjct: 134 PKEIAGLMLSAILSDTLLFKSPTTTEQDKAAAEELAE----IAGVDIE 177
>gnl|CDD|232900 TIGR00272, DPH2, diphthamide biosynthesis protein 2. This protein
has been shown in Saccharomyces cerevisiae to be one of
several required for the modification of a particular
histidine residue of translation elongation factor 2 to
diphthamide. This modified site can then become the
target for ADP-ribosylation by diphtheria toxin [Protein
fate, Protein modification and repair].
Length = 496
Score = 28.4 bits (63), Expect = 4.0
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 11/74 (14%)
Query: 174 KLVNFTPEEIAALLSC---LVFQSK-----TTTPTELPESLKQGMSIIADMNIEVESIEK 225
KL NF +I LL C + S TP EL +L + ++ + D ++ IE+
Sbjct: 326 KLANFEDIDIFVLLGCSQSGIIDSNEFYRPIVTPFELNLALSEEVTWVVDFRDSIDEIEQ 385
Query: 226 KHGVERDKSSEEAD 239
+ + +
Sbjct: 386 ---LLGGQDTISPS 396
>gnl|CDD|153234 cd03140, GATase1_PfpI_3, Type 1 glutamine amidotransferase
(GATase1)-like domain found in a subgroup of proteins
similar to PfpI from Pyrococcus furiosus. Type 1
glutamine amidotransferase (GATase1)-like domain found
in a subgroup of proteins similar to PfpI from
Pyrococcus furiosus. PfpI is an ATP-independent
intracellular proteases which may hydrolyze small
peptides to provide a nutritional source. Only Cys of
the catalytic triad typical of GATase1 domains is
conserved in this group. This Cys residue is found in
the sharp turn between a beta strand and an alpha helix
termed the nucleophile elbow.
Length = 170
Score = 27.6 bits (62), Expect = 4.5
Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 182 EIAALLSCLV----FQSKTTTPTELPESLKQGMSIIADMNIEVESIEK 225
E A L + L F+ +T +PT P + G+ ++ D +++ E
Sbjct: 13 EGAYLAALLNSYEGFEVRTVSPTGEPVTSIGGLRVVPDYSLDDLPPED 60
>gnl|CDD|131618 TIGR02567, YscW, type III secretion system chaperone YscW. This
family of proteins is found within type III secretion
operons. The protein has been characterized as a
chaperone for the outer membrane pore component YscC
(TIGR02516). YscW is a lipoprotein which is itself
localized to the outer membrane and, it is believed,
facilitates the oligomerization and localization of
YscC.
Length = 124
Score = 26.7 bits (59), Expect = 6.6
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 123 MSLYADYDSKVKVLQELNYINSQGIVQLKGNIACEMGSKNEL-LITELLFQNK 174
+S+ + KV + E +Y Q VQ + K EL L +L +Q +
Sbjct: 42 VSMCQVVEGKVLTVAEQHYRGVQLPVQYSFLLNPIQAGKGELYLRGKLSWQGQ 94
>gnl|CDD|237843 PRK14869, PRK14869, putative manganese-dependent inorganic
pyrophosphatase; Provisional.
Length = 546
Score = 27.9 bits (63), Expect = 6.8
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 12/62 (19%)
Query: 165 LITELLFQNKLVNFTPE-EIAALLSC------LVFQSKTTTPTELPESLKQGMSIIADMN 217
++ + +N + P EIA LL L+F+S TTT + E+ + ++ IA ++
Sbjct: 358 IVARMYRENGI---EPSPEIAGLLLAAILSDTLLFKSPTTTELDR-EAAEW-LAEIAGID 412
Query: 218 IE 219
E
Sbjct: 413 PE 414
>gnl|CDD|224704 COG1791, COG1791, Uncharacterized conserved protein, contains
double-stranded beta-helix domain [Function unknown].
Length = 181
Score = 27.0 bits (60), Expect = 7.3
Identities = 11/60 (18%), Positives = 23/60 (38%)
Query: 169 LLFQNKLVNFTPEEIAALLSCLVFQSKTTTPTELPESLKQGMSIIADMNIEVESIEKKHG 228
+ + +EIA LS + + T L + + II E++ + ++ G
Sbjct: 5 RIHDETKIITNQDEIAPELSKIEVSFERWEATALIKHGAEKEHIIDAYETEIDRLIRERG 64
>gnl|CDD|212680 cd10238, HSPA14-like_NBD, Nucleotide-binding domain of human HSPA14
and similar proteins. Human HSPA14 (also known as
70-kDa heat shock protein 14, HSP70L1, HSP70-4; the gene
encoding HSPA14 maps to 10p13), is ribosome-associated
and belongs to the heat shock protein 70 (HSP70) family
of chaperones that assist in protein folding and
assembly, and can direct incompetent "client" proteins
towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs). HSPA14
interacts with the J-protein MPP11 to form the mammalian
ribosome-associated complex (mRAC). HSPA14 participates
in a pathway along with Nijmegen breakage syndrome 1
(NBS1, also known as p85 or nibrin), heat shock
transcription factor 4b (HSF4b), and HSPA4 (belonging to
a different subfamily), that induces tumor migration,
invasion, and transformation. HSPA14 is a potent T
helper cell (Th1) polarizing adjuvant that contributes
to antitumor immune responses.
Length = 375
Score = 27.3 bits (61), Expect = 8.7
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 133 VKVLQELNYINSQGIVQ-LKGNIACEMGSKNELLITELLFQNKLVNFTPEEIAALL 187
VK Q L S Q K +C++ K+ E+ + K + +P+E+A L+
Sbjct: 64 VKNKQILGRSYSDPFKQKEKTESSCKIIEKDGEPKYEIFTEEKTKHVSPKEVAKLI 119
>gnl|CDD|237824 PRK14824, PRK14824, putative deoxyribonucleotide triphosphate
pyrophosphatase; Provisional.
Length = 201
Score = 27.0 bits (60), Expect = 9.4
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 200 TELPESLKQGMSIIADMNIEVESIEKKHGVERDKSS 235
T +++ +++D+ IEV S +KK VE D +
Sbjct: 7 TTNEGKVREIKRLLSDLGIEVLSPDKKIEVEEDGET 42
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
0.317 0.133 0.389
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,726,904
Number of extensions: 1169526
Number of successful extensions: 1103
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1101
Number of HSP's successfully gapped: 21
Length of query: 259
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 164
Effective length of database: 6,723,972
Effective search space: 1102731408
Effective search space used: 1102731408
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: 58 (26.1 bits)