RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3878
(299 letters)
>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase;
Provisional.
Length = 481
Score = 35.5 bits (81), Expect = 0.032
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 69 PAQLGSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSSCAATPTYSTSGDIYFSG 128
P + +P NTN++ N + ++ NN NTS S+ T++ + T + S G
Sbjct: 298 PTEAAKPAPAPSTNTNANKTNTNTNTNTNNTNTSTPSKN-TNTNTNSNTNTNSNTNANQG 356
Query: 129 SQNDNSHQLLGK--AVESHHLGSMYS 152
S N+NS+ A HLG YS
Sbjct: 357 SSNNNSNSSASAIIAEAQKHLGKAYS 382
Score = 30.5 bits (68), Expect = 1.1
Identities = 17/61 (27%), Positives = 31/61 (50%)
Query: 54 PWKKSPQSAGGNSTTPAQLGSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSSCA 113
P + + +T + + T +NTN++T +NT+T+SN N N ++ SS +
Sbjct: 308 PSTNTNANKTNTNTNTNTNNTNTSTPSKNTNTNTNSNTNTNSNTNANQGSSNNNSNSSAS 367
Query: 114 A 114
A
Sbjct: 368 A 368
Score = 28.2 bits (62), Expect = 6.2
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 40 PPPLADAAVGKGFHPWKKSPQSAGGNSTTPAQLGSLSPTSQRNTNSSTPNNTSTSSNNNN 99
P P + + N++TP++ + + + NTN+++ N + S+NNN
Sbjct: 304 PAPAPSTNTNANKTNTNTNTNTNNTNTSTPSK--NTNTNTNSNTNTNSNTNANQGSSNNN 361
Query: 100 NTSYTSRVITSS 111
+ S S +I +
Sbjct: 362 SNSSASAIIAEA 373
>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed.
Length = 637
Score = 32.3 bits (74), Expect = 0.33
Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 5/50 (10%)
Query: 100 NTSYTSRVITSSCAATPTYSTS----GDIYFSGSQNDNSHQLLGKAVESH 145
N Y+S +I + DI + ++DN ++ + VE +
Sbjct: 373 NAGYSSEIIKDESISFEEIEEKIYKIKDIL-NLEEDDNDITVIARVVEDY 421
>gnl|CDD|115579 pfam06933, SSP160, Special lobe-specific silk protein SSP160. This
family consists of several special lobe-specific silk
protein SSP160 sequences which appear to be specific to
Chironomus (Midge) species.
Length = 758
Score = 32.1 bits (72), Expect = 0.40
Identities = 21/69 (30%), Positives = 40/69 (57%)
Query: 61 SAGGNSTTPAQLGSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSSCAATPTYST 120
SA GNS++ A S S ++ N ++++ N+T+T+SN+ ++++ TS +TS + T
Sbjct: 104 SASGNSSSSANSTSNSNSTTSNNSTTSSNSTTTTSNSTSSSNSTSSGLTSGASVVSLIDT 163
Query: 121 SGDIYFSGS 129
+Y S
Sbjct: 164 CAWVYQDSS 172
Score = 29.7 bits (66), Expect = 2.2
Identities = 14/47 (29%), Positives = 29/47 (61%)
Query: 73 GSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSSCAATPTYS 119
GS S S + NS++ +N++TS+N+ +++ T+ S+ ++ T S
Sbjct: 103 GSASGNSSSSANSTSNSNSTTSNNSTTSSNSTTTTSNSTSSSNSTSS 149
Score = 28.6 bits (63), Expect = 5.3
Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 7/63 (11%)
Query: 60 QSAGGNSTTPAQLGSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSSCAATPTYS 119
QS G+++ + S S S N+NS+T NN++TSSN+ TS + TSS +T +
Sbjct: 99 QSGSGSASGNS---SSSANSTSNSNSTTSNNSTTSSNSTTTTSNS----TSSSNSTSSGL 151
Query: 120 TSG 122
TSG
Sbjct: 152 TSG 154
Score = 28.2 bits (62), Expect = 7.5
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 84 NSSTPNNTSTSSNNNNNTSYTSRVITSSCAATPTYSTS 121
N S N++++SN+ +N++ S T++ + T T STS
Sbjct: 278 NGSASANSTSNSNSTSNSTTNSNSTTTTNSTTSTNSTS 315
>gnl|CDD|131944 TIGR02898, spore_YhcN_YlaJ, sporulation lipoprotein, YhcN/YlaJ
family. YhcN and YlaJ are predicted lipoproteins that
have been detected as spore proteins but not vegetative
proteins in Bacillus subtilis. Both appear to be
expressed under control of the RNA polymerase sigma-G
factor. The YlaJ-like members of this family have a
low-complexity, strongly acidic 40-residue C-terminal
domain that is not included in the seed alignment for
this model. A portion of the low-complexity region
between the lipoprotein signal sequence and the main
conserved region of the protein family was also excised
from the seed alignment [Cellular processes, Sporulation
and germination].
Length = 158
Score = 30.4 bits (69), Expect = 0.54
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 68 TPAQLGSLSPTSQRNTNSSTPNNTSTSSNNNNN 100
T AQ + + TN + NN ++ N+ N
Sbjct: 16 TNAQKKNPPNNNVGETNVMSKNNNGMNTTNDTN 48
>gnl|CDD|184465 PRK14032, PRK14032, citrate synthase; Provisional.
Length = 447
Score = 31.4 bits (72), Expect = 0.63
Identities = 11/22 (50%), Positives = 17/22 (77%), Gaps = 2/22 (9%)
Query: 99 NNTSYTSRVITSSCAATPTYST 120
NN+++T+RV++SS T TYS
Sbjct: 242 NNSTFTTRVVSSS--GTDTYSA 261
>gnl|CDD|99866 cd06113, citrate_synt_like_1_2, Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) and
oxalacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. This group also includes CS proteins
which functions as a 2-methylcitrate synthase (2MCS).
2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
and OAA to form 2-methylcitrate and CoA during
propionate metabolism. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS. The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) a carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) nucleophilic attack of this carbanion on
OAA to generate citryl-CoA, and c) hydrolysis of
citryl-CoA to produce citrate and CoA. CSs are found in
two structural types: type I (homodimeric) and type II
CSs (homohexameric). Type II CSs are unique to
gram-negative bacteria. Type I CSs are found in eukarya,
gram-positive bacteria, archaea, and in some
gram-negative bacteria. Type I CS is active as a
homodimer, both subunits participating in the active
site. Type II CS is a hexamer of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism. This subgroup includes both
gram-positive and gram-negative bacteria.
Length = 406
Score = 31.1 bits (71), Expect = 0.65
Identities = 11/22 (50%), Positives = 17/22 (77%), Gaps = 2/22 (9%)
Query: 99 NNTSYTSRVITSSCAATPTYST 120
NN+++T+RV++SS T TYS
Sbjct: 212 NNSTFTTRVVSSS--GTDTYSA 231
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 30.7 bits (69), Expect = 1.0
Identities = 22/138 (15%), Positives = 45/138 (32%), Gaps = 9/138 (6%)
Query: 31 QCNKLSNKSPPPLADAAVGKGFHPWKKSPQSAGGNSTTPAQLGSLSPTSQRNTNSSTPNN 90
N S + L V H K P S+ N + S S + + S+ +
Sbjct: 275 INNHHSKHADSKLQTIEV-IENHSNKSRPSSSSTNGSKETTSNSSSAAAGSIGSKSSKSA 333
Query: 91 TSTSSNNNNNTSYTSRVITSSC-AATPTYSTSGDIYFSGSQNDNSHQLLGKAVESHHLGS 149
++ N +N++ + S +++ + + S + +S K S
Sbjct: 334 KHSNRNKSNSSPKSHSSANGSVPSSSVSDNESKQ---KRASKSSSGARDSKKDAS----G 386
Query: 150 MYSRHPYESWPFNTMTSS 167
M + E+ S+
Sbjct: 387 MSANGTVENCIPENKIST 404
>gnl|CDD|223031 PHA03273, PHA03273, envelope glycoprotein C; Provisional.
Length = 486
Score = 30.0 bits (67), Expect = 1.6
Identities = 27/126 (21%), Positives = 45/126 (35%), Gaps = 17/126 (13%)
Query: 58 SPQSAGGNSTTPAQLGSLSP------TSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSS 111
S S+ NS +P TS + T + ST++N +T+ S+ +
Sbjct: 29 STSSSIENSDNSTAEMQSTPATPTHTTSNLTSPFGTGTDNSTNANGTESTTQASQPHSHE 88
Query: 112 CAATPTYSTSGDIYFSGSQNDNSHQLLGKAVESHHLGSMYSRHPYESWPFNTMTSSSHHK 171
T T S Y+ + + +V ++ S + E + N T S
Sbjct: 89 TTITCTKSLISVPYYKSVDMNCT-----TSVGVNY-----SEYRLEIY-LNQRTPFSGTP 137
Query: 172 PGDGMN 177
PGD N
Sbjct: 138 PGDEEN 143
>gnl|CDD|236345 PRK08870, flgL, flagellar hook-associated protein FlgL; Reviewed.
Length = 404
Score = 29.9 bits (68), Expect = 1.9
Identities = 13/66 (19%), Positives = 21/66 (31%), Gaps = 6/66 (9%)
Query: 69 PAQLGSLSPTSQRNTNSSTPNNTS------TSSNNNNNTSYTSRVITSSCAATPTYSTSG 122
+ G+ S T+ S P N T + +Y + T + Y
Sbjct: 199 ASNTGTGLLGSASITDPSDPVNGDTYTITFTDNGAGGTNTYVTDSSTGTVVTAQAYDAGQ 258
Query: 123 DIYFSG 128
I F+G
Sbjct: 259 PINFNG 264
>gnl|CDD|232855 TIGR00173, menD,
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
carboxylic-acid synthase. MenD was thought until
recently to act as SHCHC synthase, but has recently
been shown to act instead as SEPHCHC synthase.
Conversion of SEPHCHC into SHCHC and pyruvate may occur
spontaneously but is catalyzed efficiently, at least in
some organisms, by MenH (see TIGR03695). 2-oxoglutarate
decarboxylase/SHCHC synthase (menD) is a thiamine
pyrophosphate enzyme involved in menaquinone
biosynthesis [Biosynthesis of cofactors, prosthetic
groups, and carriers, Menaquinone and ubiquinone].
Length = 430
Score = 29.5 bits (67), Expect = 2.3
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 18 PGLRGTPLAMLAAQCNKL 35
PG R TPLA+ A+ +L
Sbjct: 21 PGSRSTPLALALAEHPRL 38
>gnl|CDD|187664 cd09763, DHRS1-like_SDR_c, human dehydrogenase/reductase (SDR
family) member 1 (DHRS1) -like, classical (c) SDRs.
This subgroup includes human DHRS1 and related proteins.
These are members of the classical SDR family, with a
canonical Gly-rich NAD-binding motif and the typical
YXXXK active site motif. However, the rest of the
catalytic tetrad is not strongly conserved. DHRS1 mRNA
has been detected in many tissues, liver, heart,
skeletal muscle, kidney and pancreas; a longer
transcript is predominantly expressed in the liver , a
shorter one in the heart. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 265
Score = 28.2 bits (63), Expect = 4.5
Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 167 SSHHKPGDGMNTGWWDVPAGGWLDM-SGGMHAQMAANYAA 205
++ G+ +W+ P W D+ + G+ A A + A
Sbjct: 92 AAVQLILVGVAKPFWEEPPTIWDDINNVGLRAHYACSVYA 131
>gnl|CDD|240410 PTZ00418, PTZ00418, Poly(A) polymerase; Provisional.
Length = 593
Score = 28.6 bits (64), Expect = 4.7
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 56 KKSPQSAGGNSTTPAQLGSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYT 104
K + ++ ++TT Q GS TS N+N S+P +ST N ++TS T
Sbjct: 543 KANTKTNTSSATTSGQSGSSGSTSNSNSNESSPTMSSTELLNVSSTSTT 591
>gnl|CDD|240430 PTZ00473, PTZ00473, Plasmodium Vir superfamily; Provisional.
Length = 420
Score = 28.3 bits (63), Expect = 6.1
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 7/85 (8%)
Query: 58 SPQSAGGNSTTPAQ-LGSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSSCAAT- 115
S +S G + + G S + + ++ST + ST ++ S + T ++T
Sbjct: 335 SSESIRGFTYDSSTTYGGSSYGTSQTDSTSTYGSRSTFDSSTGGGSQSGGGSTYGGSSTF 394
Query: 116 --PTYSTS---GDIYFSGSQNDNSH 135
+ +S G YF Q
Sbjct: 395 DGSSRGSSDSFGVSYFGPQQTVGFS 419
>gnl|CDD|115714 pfam07078, FYTT, Forty-two-three protein. This family consists of
several mammalian proteins of around 320 residues in
length called 40-2-3 proteins. The function of this
family is unknown.
Length = 316
Score = 27.8 bits (61), Expect = 6.5
Identities = 14/62 (22%), Positives = 27/62 (43%)
Query: 35 LSNKSPPPLADAAVGKGFHPWKKSPQSAGGNSTTPAQLGSLSPTSQRNTNSSTPNNTSTS 94
+S + PPL+D + + F K+ N + +L +Q N ++ P N + +
Sbjct: 115 ISPMNRPPLSDKNIERYFPALKRKANLLRQNEVQRKPVAALKRPNQLNRKNNIPANFTRN 174
Query: 95 SN 96
N
Sbjct: 175 GN 176
>gnl|CDD|185159 PRK15247, PRK15247, putative fimbrial usher protein StbD;
Provisional.
Length = 441
Score = 27.9 bits (62), Expect = 6.5
Identities = 28/111 (25%), Positives = 48/111 (43%), Gaps = 18/111 (16%)
Query: 30 AQCNKLSNKSPPPLADAAVGKGFHPWKKSPQSAGGNSTTPAQLGSLSPTSQRNTNSSTPN 89
+ C K+++KS L+DAA+ G+ + G T +G + S N+ + P+
Sbjct: 22 SSCIKVTDKSA--LSDAAIKAGY----TAQNWIGATDTNTGNIGLPTVISVSNSETFQPS 75
Query: 90 NTSTSS------NNNNNTSYTSRVITSSCAATPT------YSTSGDIYFSG 128
T +S T Y+S+ + C + YST+GD F+G
Sbjct: 76 GTLLASGIGNFLTAATGTPYSSKQVLYRCDSADAGKLYEMYSTNGDSAFAG 126
>gnl|CDD|197360 cd10052, Reelin_repeat_8_subrepeat_2, C-terminal subrepeat of
tandem repeat unit 8 of reelin and related proteins.
Reelin is an extracellular glycoprotein involved in
neuronal development, specifically in the brain cortex.
It contains 8 tandemly repeated units, each of which is
composed of two highly similar subrepeats and a central
EGF domain. This model characterizes the C-terminal
subrepeat, which directly contacts the N-terminal
subrepeat and the EGF domain in a compact arrangement.
Consecutive reelin repeat units are packed together to
form an overall rod-like molecular structure. Reelin
repeats 5 and 6 are reported to interact with neuronal
receptors, the apolipoprotein E receptor 2 (ApoER2) and
the very-low-density lipoprotein receptor (VLDLR),
triggering a signaling cascade upon binding and
subsequent tyrosine phosphorylation of the cytoplasmic
disabled-1 (Dab1).
Length = 161
Score = 27.5 bits (61), Expect = 6.7
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 71 QLGSLSPTSQRNTNSSTPN 89
Q+GS S T N N S+P
Sbjct: 70 QIGSRSQTDSCNINLSSPR 88
>gnl|CDD|234493 TIGR04189, surface_SprA, cell surface protein SprA. SprA is a cell
surface protein widely distributed in the Bacteroidetes
lineage. In Flavobacterium johnsoniae, a species that
shows gliding motility, mutation disrupts gliding.
Length = 2315
Score = 28.1 bits (63), Expect = 7.9
Identities = 10/61 (16%), Positives = 18/61 (29%), Gaps = 1/61 (1%)
Query: 72 LGSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRV-ITSSCAATPTYSTSGDIYFSGSQ 130
LG +N N P + +N N Y + + I + T +
Sbjct: 306 LGEPESLYTKNNNPIGPQGPNRLPDNGANNLYPTLIGIPNGIRDIATVVQGFGGLVQQGR 365
Query: 131 N 131
+
Sbjct: 366 D 366
>gnl|CDD|233185 TIGR00918, 2A060602, The Eukaryotic (Putative) Sterol Transporter
(EST) Family.
Length = 1145
Score = 27.9 bits (62), Expect = 8.4
Identities = 19/118 (16%), Positives = 33/118 (27%), Gaps = 17/118 (14%)
Query: 55 WKKSPQSAGGNSTTPAQLGSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSSCAA 114
+ PQ+ S P + T Q T ++N S +
Sbjct: 581 IQIEPQAYADGSAPPVYSSHMQSTVQLRTEYDPGTQHYYTTNEPR----------SHLSV 630
Query: 115 TPTYSTSGDIYFSGSQNDNSHQLLGKAVESHHLGSMYSRHPYESWPFNTMTSSSHHKP 172
P+ S ++ LL + +S + P W T + H+ P
Sbjct: 631 QPSDPLSCQSPDIAG---STRDLLSQFEDS---KAACLSLPCARWTLATF-AEKHYAP 681
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
0.311 0.124 0.382
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,407,754
Number of extensions: 1257537
Number of successful extensions: 1700
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1613
Number of HSP's successfully gapped: 94
Length of query: 299
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 203
Effective length of database: 6,679,618
Effective search space: 1355962454
Effective search space used: 1355962454
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 59 (26.7 bits)