RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18090
(421 letters)
>gnl|CDD|214733 smart00584, TLDc, domain in TBC and LysM domain containing
proteins.
Length = 165
Score = 137 bits (348), Expect = 4e-39
Identities = 58/171 (33%), Positives = 84/171 (49%), Gaps = 8/171 (4%)
Query: 207 MSILDYSHIMFLNLNLMPEFQ-KQWRLLFSSQFQGESFTRLM-ACAINQGPLLVLVKDDK 264
SIL + +N +L + W LL+SS G S L + P L+++KD
Sbjct: 1 SSILSEEILALINSHLPTRAEGYPWTLLYSSSQHGYSLNTLYRKVEGYRPPTLLIIKDTD 60
Query: 265 ANIFGAYASTNLTLCPKFYGDQNSFLFTLKPDMKVFNSSGFNENFIYLNSNQQTLPNGLG 324
+FGAYAS + FYG SFLF L P V++ +G + Y+N +LP G G
Sbjct: 61 GEVFGAYASQAWRVSDHFYGTGESFLFQLNPKFVVYDWTG-KNKYYYINGTPDSLPIGGG 119
Query: 325 FGGQFEYWGLWIDSEYGQGECNKTCSTFKDYQMLSHDKHFKIMHIELWGVG 375
GG +GLWID + G + C TF + + + + F I+ IE+WG G
Sbjct: 120 GGG----FGLWIDEDLNHGSSSH-CKTFGNPPLSTKQEDFLILDIEVWGFG 165
>gnl|CDD|219457 pfam07534, TLD, TLD. This domain is predicted to be an enzyme and
is often found associated with pfam01476.
Length = 136
Score = 121 bits (305), Expect = 4e-33
Identities = 57/145 (39%), Positives = 80/145 (55%), Gaps = 10/145 (6%)
Query: 232 LLFSSQFQGESFTRLMACAINQGPLLVLVKDDKANIFGAYASTNLTL-CPKFYGDQNSFL 290
LL+SS G S + N+GP L++VKDD +FGA+ S KFYGD SFL
Sbjct: 1 LLYSSSRHGSSLNTFLEKCDNKGPTLLIVKDDDGYVFGAFLSQPWKNSGKKFYGDGESFL 60
Query: 291 FTLKPDMKVFNSSGFNENFIYLNSNQQTLPNGLGFGGQFEYWGLWIDSEYGQGECNKTCS 350
F+L P KV+ +G +N Y N+ +GLGFGG ++ LWIDS+ G C
Sbjct: 61 FSLSPKFKVYKWTG--KNNAYFNAT-----SGLGFGGGGKF-ALWIDSDLEFGYSR-HCG 111
Query: 351 TFKDYQMLSHDKHFKIMHIELWGVG 375
TF + + + FKI+ +E+WG+G
Sbjct: 112 TFGNPPLSGSQERFKILDLEVWGLG 136
>gnl|CDD|227471 COG5142, OXR1, Oxidation resistance protein [DNA replication,
recombination, and repair].
Length = 212
Score = 69.5 bits (170), Expect = 1e-13
Identities = 43/162 (26%), Positives = 67/162 (41%), Gaps = 22/162 (13%)
Query: 229 QWRLLFSSQFQGESF-TRLMACAINQGPL-----LVLVKDDKANIFGAYASTNLTLCPKF 282
WRLL+S G S T + N+ P ++ +D ++FGA+ + +
Sbjct: 58 SWRLLYSLFENGFSLRTFYESFGENEWPFRRVGFVLACRDKDGDLFGAFFEDRIRPARHY 117
Query: 283 YGDQNSFLFTL--KPDMK-------VFNSSGFNENFIYLNSNQQTLPNGLGFGGQFEYWG 333
YG FL+ +P + V+ SG IY P+ L FG +G
Sbjct: 118 YGRDEMFLWKAARRPADRLADKEVAVYPISGGKGFGIYCT------PDFLAFGCGGGRYG 171
Query: 334 LWIDSEYGQGECNKTCSTFKDYQMLSHDKHFKIMHIELWGVG 375
L ID GE + TF + + S F+I+++ELW V
Sbjct: 172 LLIDKSLLDGESHP-VETFGNCLLSSKGHFFRIVYLELWLVQ 212
>gnl|CDD|227623 COG5307, COG5307, SEC7 domain proteins [General function prediction
only].
Length = 1024
Score = 32.8 bits (75), Expect = 0.40
Identities = 17/93 (18%), Positives = 38/93 (40%), Gaps = 11/93 (11%)
Query: 38 KDVLTK-VDVFELWSMEIKDSLINFYLKYYFPDKTEKID--LSTFISLYYELDGSNIDRK 94
VL + + +F+ ++I ++L + P + ++ID L F YY + K
Sbjct: 331 NAVLREFISLFDFKGLDIDEALRKLLQSFRLPGEAQQIDRILEAFSDKYYSDNPKKFSSK 390
Query: 95 VEILLCFIGSYGDLINYVQALLNSCLFIYQSRD 127
+ +I ++ ++ LN+ L +
Sbjct: 391 PDS--VYILAFSLIM------LNTDLHNPNIKA 415
>gnl|CDD|237065 PRK12334, PRK12334, nucleoside triphosphate pyrophosphohydrolase;
Reviewed.
Length = 277
Score = 30.8 bits (70), Expect = 1.3
Identities = 16/41 (39%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 381 AEEKGERSVLDADPTASALLELAGKT---KHSAGLREPDVE 418
A EK SVLD P L LA K AGL P
Sbjct: 179 AAEKARTSVLDGVPLGQPALALAAKVLSRARKAGLPVPLAP 219
>gnl|CDD|233374 TIGR01357, aroB, 3-dehydroquinate synthase. This model represents
3-dehydroquinate synthase, the enzyme catalyzing the
second of seven steps in the shikimate pathway of
chorismate biosynthesis. Chorismate is the last common
intermediate in the biosynthesis of all three aromatic
amino acids [Amino acid biosynthesis, Aromatic amino
acid family].
Length = 344
Score = 29.9 bits (68), Expect = 2.2
Identities = 28/104 (26%), Positives = 39/104 (37%), Gaps = 7/104 (6%)
Query: 11 GSGSLKKNLSRKIKPEDVKKIKSLTNGKDVLTKVDVFELWSMEIKDSLINFYLKYYFPDK 70
G G L + + +P + I T K+ E +L LK PD
Sbjct: 6 GEGLLDQLVEELAEPSKLVIITDETVADLYADKLL-------EALQALGYNVLKLTVPDG 58
Query: 71 TEKIDLSTFISLYYELDGSNIDRKVEILLCFIGSYGDLINYVQA 114
E L T LY +L + +DR I+ G GDL +V A
Sbjct: 59 EESKSLETVQRLYDQLLEAGLDRSSTIIALGGGVVGDLAGFVAA 102
>gnl|CDD|216057 pfam00680, RdRP_1, RNA dependent RNA polymerase.
Length = 479
Score = 30.3 bits (69), Expect = 2.2
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 27 DVKKIKSLTNGKDVLTKVD-VFELWSMEIKDSLINFYLKYYFPDKTE 72
D + +K ++ G D L V + ++K+ L L F DKT
Sbjct: 329 DDEILKFISYGDDNLISVKPEVDSVLDKLKEHLAELGLTITFADKTS 375
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 29.3 bits (67), Expect = 2.4
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 7/29 (24%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLS 170
G+++VY D N +F++L KWL+
Sbjct: 75 GAILVY-------DVTNRESFENLDKWLN 96
>gnl|CDD|135648 PRK05898, dnaE, DNA polymerase III DnaE; Validated.
Length = 971
Score = 29.4 bits (66), Expect = 4.0
Identities = 18/90 (20%), Positives = 35/90 (38%), Gaps = 3/90 (3%)
Query: 3 NEHSNKKQGSGSLKKNLSRKIKPEDVKKIKSLTNGKDVLTKVDVFELWSMEIKDSLINFY 62
N + + L I +D+K+I+ + V+E+ + K+ ++FY
Sbjct: 866 NSLNYANYKNEIDYNELKYTI--KDIKEIELKNTNYETNIFAQVYEIKQSKTKNGNLSFY 923
Query: 63 LKYYFPDKTEKID-LSTFISLYYELDGSNI 91
L+ +K + I L E+D I
Sbjct: 924 LETLINNKKKTITIFQHSKYLIDEIDIGGI 953
>gnl|CDD|216326 pfam01142, TruD, tRNA pseudouridine synthase D (TruD). TruD is
responsible for synthesis of pseudouridine from
uracil-13 in transfer RNAs. The structure of TruD
reveals an overall V-shaped molecule which contains an
RNA-binding cleft.
Length = 336
Score = 29.1 bits (66), Expect = 4.6
Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 1/52 (1%)
Query: 371 LWGVGIPPPTAEEKG-ERSVLDADPTASALLELAGKTKHSAGLREPDVELEN 421
L G G+ E E+ +L + EL K R ++ EN
Sbjct: 256 LPGRGVLLAEGEAGELEQEILAEEGITPEDFELLPKLGLKGERRPLRLKPEN 307
>gnl|CDD|185661 PTZ00483, PTZ00483, proliferating cell nuclear antigen;
Provisional.
Length = 264
Score = 29.1 bits (65), Expect = 4.6
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 206 TMSILDYSHIMFLNLNLMPEFQKQWR 231
M +D SHI ++LNL P+F + +R
Sbjct: 35 KMQAMDNSHISLIHLNLAPDFFQLYR 60
>gnl|CDD|200599 cd10977, CE4_PuuE_SpCDA1, Catalytic domain of bacterial PuuE
allantoinases, Schizosaccharomyces pombe chitin
deacetylase 1 (SpCDA1), and similar proteins.
Allantoinase (EC 3.5.2.5) can hydrolyze
allantoin((2,5-dioxoimidazolidin-4-yl)urea), one of the
most important nitrogen carrier for some plants, soil
animals, and microorganisms, to allantoate. DAL1 gene
from Saccharomyces cerevisiae encodes an allantoinase.
However, some organisms possess allantoinase activity
but lack DAL1 allantoinase. In those organisms, a
defective allantoinase gene, named puuE (purine
utilization E), encodes an allantoinase that
specifically catalyzes the hydrolysis of (S)-allantoin
into allantoic acid. PuuE allantoinase is related to
polysaccharide deacetylase (DCA), one member of the
carbohydrate esterase 4 (CE4) superfamily, that removes
N-linked or O-linked acetyl groups of cell wall
polysaccharides, and lacks sequence similarity with the
known DAL1 allantoinase that belongs to the
amidohydrolase superfamily. PuuE allantoinase functions
as a homotetramer. Its monomer is composed of a
7-stranded barrel with detectable sequence similarity to
the 6-stranded barrel NodB homology domain of DCAs. It
appears to be metal-independent and acts on a small
substrate molecule, which is distinct from the common
features of DCAs that are normally metal ion dependent
and recognize multimeric substrates. This family also
includes a chitin deacetylase 1 (SpCDA1) encoded by the
Schizosaccharomyces pombe cda1 gene. Although the
general function of chitin deacetylase (CDA) is the
synthesis of chitosan from chitin, a polymer of N-acetyl
glucosamine, to build up the proper ascospore wall, the
actual function of SpCDA1 might involve allantoin
hydrolysis. It is likely orthologous to PuuE
allantoinase, whereas it is more distantly related to
the CDAs found in other fungi, such as Saccharomyces
cerevisiae and Mucor rouxii. Those CDAs are similar with
rizobial NodB protein and are not included in this
family.
Length = 273
Score = 28.8 bits (65), Expect = 5.3
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 382 EEKGERSVLDADPTASALLE 401
EE GERS+L D + + L
Sbjct: 16 EEGGERSILHGDGASESFLS 35
>gnl|CDD|177619 PHA03383, PHA03383, PCNA-like protein; Provisional.
Length = 262
Score = 28.3 bits (63), Expect = 6.5
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 126 RDDKELWSSLNIDSDKGSLIVYANYLCMGDCNNEITF--DSLQKWLSTTHEIAYLHKYVL 183
RD + L I + ++Y C+ D ++ T DS ++ Y K+ L
Sbjct: 156 RDMSNITDDLEITKKGKEVSFRSDYTCVTDFASQETIIGDSDNGQITCNESPDYTGKFSL 215
Query: 184 SHMFGF 189
++ F
Sbjct: 216 KYLTSF 221
>gnl|CDD|213319 cd05972, MACS_like, Medium-chain acyl-CoA synthetase (MACS or
ACSM). MACS catalyzes the two-step activation of medium
chain fatty acids (containing 4-12 carbons). The
carboxylate substrate first reacts with ATP to form an
acyl-adenylate intermediate, which then reacts with CoA
to produce an acyl-CoA ester. The acyl-CoA is a key
intermediate in many important biosynthetic and
catabolic processes.
Length = 430
Score = 28.5 bits (64), Expect = 8.5
Identities = 8/25 (32%), Positives = 9/25 (36%)
Query: 330 EYWGLWIDSEYGQGECNKTCSTFKD 354
GL I YGQ E + F
Sbjct: 219 AATGLPIRDGYGQTETGLLVANFPG 243
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 27.5 bits (62), Expect = 8.7
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 142 GSLIVYANYLCMGDCNNEITFDSLQKWLSTTHEIA 176
G+L+VY D + TF+++++WL + A
Sbjct: 78 GALLVY-------DITKKSTFENVERWLKELRDHA 105
>gnl|CDD|179133 PRK00809, PRK00809, hypothetical protein; Provisional.
Length = 144
Score = 27.3 bits (61), Expect = 9.8
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 7 NKKQGSGSLKKNLSRKIKPEDVKKIKS 33
NKKQ SG L+ R I ED K I+
Sbjct: 117 NKKQWSGHLRNRAMRPIPEEDYKLIEE 143
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 0.137 0.415
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,333,439
Number of extensions: 2061360
Number of successful extensions: 1577
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1565
Number of HSP's successfully gapped: 32
Length of query: 421
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 322
Effective length of database: 6,546,556
Effective search space: 2107991032
Effective search space used: 2107991032
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 (21.7 bits)
S2: 60 (26.9 bits)