RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10634
(303 letters)
>gnl|CDD|238103 cd00176, SPEC, Spectrin repeats, found in several proteins involved
in cytoskeletal structure; family members include
spectrin, alpha-actinin and dystrophin; the spectrin
repeat forms a three helix bundle with the second helix
interrupted by proline in some sequences; the repeats
are independent folding units; tandem repeats are found
in differing numbers and arrange in an antiparallel
manner to form dimers; the repeats are defined by a
characteristic tryptophan (W) residue in helix A and a
leucine (L) at the carboxyl end of helix C and separated
by a linker of 5 residues; two copies of the repeat are
present here.
Length = 213
Score = 116 bits (292), Expect = 2e-31
Identities = 74/217 (34%), Positives = 109/217 (50%), Gaps = 29/217 (13%)
Query: 84 LLYQYLRDVDDEMQWLLEKEPLAVSTDLGNSLTAVQSLQKKHQALETELASREPVVSALA 143
L Q+LRD D+ WL EKE L STD G+ L +V++L KKH+ALE ELA+ E V AL
Sbjct: 1 KLQQFLRDADELEAWLSEKEELLSSTDYGDDLESVEALLKKHEALEAELAAHEERVEALN 60
Query: 144 SRAKQMSRSAHFAAARIEGATSALQDKLASLRNAASVRRLRLLDALESQMLYLASGYLES 203
+Q+ H A I+ L + LR A RR RL +AL+ Q
Sbjct: 61 ELGEQLIEEGHPDAEEIQERLEELNQRWEELRELAEERRQRLEEALDLQ----------- 109
Query: 204 NLLNPMSLWKTKHSLLIFQFYAEVAEAEVWLKEKKPILHSSDFGRDEDSVLSLIKKLESL 263
QF+ + + E WL+EK+ L S D G+D +SV L+KK + L
Sbjct: 110 ------------------QFFRDADDLEQWLEEKEAALASEDLGKDLESVEELLKKHKEL 151
Query: 264 ERELVSFQHTVGHLSKLCQSLLDRNHFDSKNISKKQV 300
E EL + + + L++L + LL+ H D+ ++++
Sbjct: 152 EEELEAHEPRLKSLNELAEELLEEGHPDADEEIEEKL 188
Score = 87.5 bits (217), Expect = 1e-20
Identities = 50/128 (39%), Positives = 69/128 (53%), Gaps = 1/128 (0%)
Query: 63 HRYRSLQEPMQIRRDNLEDALLLYQYLRDVDDEMQWLLEKEPLAVSTDLGNSLTAVQSLQ 122
R+ L+E + RR LE+AL L Q+ RD DD QWL EKE S DLG L +V+ L
Sbjct: 86 QRWEELRELAEERRQRLEEALDLQQFFRDADDLEQWLEEKEAALASEDLGKDLESVEELL 145
Query: 123 KKHQALETELASREPVVSALASRAKQMSRSAHFAAAR-IEGATSALQDKLASLRNAASVR 181
KKH+ LE EL + EP + +L A+++ H A IE L ++ L A R
Sbjct: 146 KKHKELEEELEAHEPRLKSLNELAEELLEEGHPDADEEIEEKLEELNERWEELLELAEER 205
Query: 182 RLRLLDAL 189
+ +L +AL
Sbjct: 206 QKKLEEAL 213
>gnl|CDD|197544 smart00150, SPEC, Spectrin repeats.
Length = 101
Score = 85.8 bits (213), Expect = 3e-21
Identities = 40/100 (40%), Positives = 53/100 (53%)
Query: 86 YQYLRDVDDEMQWLLEKEPLAVSTDLGNSLTAVQSLQKKHQALETELASREPVVSALASR 145
Q+LRD D+ WL EKE L S DLG L +V++L KKH+A E EL + E V AL
Sbjct: 1 QQFLRDADELEAWLEEKEQLLASEDLGKDLESVEALLKKHEAFEAELEAHEERVEALNEL 60
Query: 146 AKQMSRSAHFAAARIEGATSALQDKLASLRNAASVRRLRL 185
+Q+ H A IE L ++ L+ A RR +L
Sbjct: 61 GEQLIEEGHPDAEEIEERLEELNERWEELKELAEERRQKL 100
Score = 65.8 bits (161), Expect = 9e-14
Identities = 29/78 (37%), Positives = 49/78 (62%)
Query: 222 QFYAEVAEAEVWLKEKKPILHSSDFGRDEDSVLSLIKKLESLERELVSFQHTVGHLSKLC 281
QF + E E WL+EK+ +L S D G+D +SV +L+KK E+ E EL + + V L++L
Sbjct: 2 QFLRDADELEAWLEEKEQLLASEDLGKDLESVEALLKKHEAFEAELEAHEERVEALNELG 61
Query: 282 QSLLDRNHFDSKNISKKQ 299
+ L++ H D++ I ++
Sbjct: 62 EQLIEEGHPDAEEIEERL 79
>gnl|CDD|215918 pfam00435, Spectrin, Spectrin repeat. Spectrin repeat-domains are
found in several proteins involved in cytoskeletal
structure. These include spectrin, alpha-actinin and
dystrophin. The sequence repeat used in this family is
taken from the structural repeat in reference. The
spectrin domain- repeat forms a three helix bundle. The
second helix is interrupted by proline in some
sequences. The repeats are defined by a characteristic
tryptophan (W) residue at position 17 in helix A and a
leucine (L) at 2 residues from the carboxyl end of helix
C. Although the domain occurs in ultiple repeats along
sequences, the domains are actually stable on their own
- ie they act, biophysically, like domains rather than
repeats that along function when aggregated.
Length = 105
Score = 83.9 bits (208), Expect = 2e-20
Identities = 41/105 (39%), Positives = 60/105 (57%)
Query: 83 LLLYQYLRDVDDEMQWLLEKEPLAVSTDLGNSLTAVQSLQKKHQALETELASREPVVSAL 142
LLL Q+ RD DD W+ EKE L S D G L +VQ+L KKH+ALE ELA+ + V AL
Sbjct: 1 LLLQQFFRDADDLESWIEEKEALLSSEDYGKDLESVQALLKKHKALEAELAAHQDRVEAL 60
Query: 143 ASRAKQMSRSAHFAAARIEGATSALQDKLASLRNAASVRRLRLLD 187
A+++ H+A+ I+ L ++ L A+ R+ +L +
Sbjct: 61 NELAEKLIAEGHYASEEIQERLEELNERWEQLLELAAERKQKLEE 105
Score = 63.1 bits (154), Expect = 8e-13
Identities = 30/82 (36%), Positives = 54/82 (65%)
Query: 218 LLIFQFYAEVAEAEVWLKEKKPILHSSDFGRDEDSVLSLIKKLESLERELVSFQHTVGHL 277
LL+ QF+ + + E W++EK+ +L S D+G+D +SV +L+KK ++LE EL + Q V L
Sbjct: 1 LLLQQFFRDADDLESWIEEKEALLSSEDYGKDLESVQALLKKHKALEAELAAHQDRVEAL 60
Query: 278 SKLCQSLLDRNHFDSKNISKKQ 299
++L + L+ H+ S+ I ++
Sbjct: 61 NELAEKLIAEGHYASEEIQERL 82
>gnl|CDD|223152 COG0074, SucD, Succinyl-CoA synthetase, alpha subunit [Energy
production and conversion].
Length = 293
Score = 32.2 bits (74), Expect = 0.24
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 133 ASREPVVSALASR-AKQMSRSAHFAAARIEGATSALQDKLASLRNA 177
A+R+PVV+ +A R A + R H A A + G + K+A+L A
Sbjct: 226 ATRKPVVAYIAGRTAPEGKRMGH-AGAIVSGGKGTAESKIAALEAA 270
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 31.6 bits (72), Expect = 0.55
Identities = 38/215 (17%), Positives = 82/215 (38%), Gaps = 20/215 (9%)
Query: 64 RYRSLQEPM---QIRRDNLEDALLLY-QYLRDVDDEMQWLLEKEPLAVSTDLGNSLTAVQ 119
++E + + +LE ++ + L D ++ + LE E + ++ ++
Sbjct: 288 EQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLA-KLEAEIDKLLAEIEELEREIE 346
Query: 120 SLQKKHQALETELASREPVVSALASRAKQMSRSAHFAAARIEGATSALQDKLASL---RN 176
+K+ L E A + + L + +++ + FA R E ++KL L N
Sbjct: 347 EERKRRDKLTEEYAELKEELEDLRAELEEVDKE--FAETRDE--LKDYREKLEKLKREIN 402
Query: 177 AASVRRLRLLDALESQMLYLASGYLESNLLNPMSLWKTKHSLLIFQFYAEVAEAEVWLKE 236
RL + E Q L L ++ + + + E E+ +E
Sbjct: 403 ELKRELDRLQE--ELQRLSEELADLN------AAIAGIEAKINELEEEKEDKALEIKKQE 454
Query: 237 KKPILHSSDFGRDEDSVLSLIKKLESLERELVSFQ 271
K ++D + E + L ++ + +E+EL Q
Sbjct: 455 WKLEQLAADLSKYEQELYDLKEEYDRVEKELSKLQ 489
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 31.6 bits (72), Expect = 0.62
Identities = 36/207 (17%), Positives = 66/207 (31%), Gaps = 15/207 (7%)
Query: 75 RRDNLEDALLLYQYLRDVDDEMQWLLEKEPLAVSTDLGNSLTAVQSLQKKH-------QA 127
R NLE L + + + L +E + L ++SL+ + +
Sbjct: 310 RLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEE 369
Query: 128 LETELASREPVVSALASRAKQMSRSAHFAAARIEGATSALQDKLASLRNAASVRRLRLLD 187
LE+ L E + L S+ Q+ IE + L+ L
Sbjct: 370 LESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKK 429
Query: 188 ALESQMLYLASGYLESNLLNPMSLWKTKHSLLIFQFYAEVAEAEVWLKEKKPILHSSDFG 247
E+++ L + E L + + L + E E+ E+
Sbjct: 430 LEEAELKELQAELEELE----EELEELQEELERLEEALEELREELEEAEQA----LDAAE 481
Query: 248 RDEDSVLSLIKKLESLERELVSFQHTV 274
R+ + + + LE L+ L F V
Sbjct: 482 RELAQLQARLDSLERLQENLEGFSEGV 508
>gnl|CDD|236165 PRK08147, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 547
Score = 30.4 bits (69), Expect = 1.3
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 140 SALASRAKQMSRSAHFAAARIEGATSALQDKLASLRNAAS 179
S L +R +QMS+ + + ++ +QD SL+ S
Sbjct: 83 SGLTTRYEQMSKIDNLLSDSTNSLSTTMQDFFTSLQTLVS 122
>gnl|CDD|217843 pfam04012, PspA_IM30, PspA/IM30 family. This family includes PspA
a protein that suppresses sigma54-dependent
transcription. The PspA protein, a negative regulator of
the Escherichia coli phage shock psp operon, is produced
when virulence factors are exported through secretins in
many Gram-negative pathogenic bacteria and its homologue
in plants, VIPP1, plays a critical role in thylakoid
biogenesis, essential for photosynthesis. Activation of
transcription by the enhancer-dependent bacterial
sigma(54) containing RNA polymerase occurs through ATP
hydrolysis-driven protein conformational changes enabled
by activator proteins that belong to the large AAA(+)
mechanochemical protein family. It has been shown that
PspA directly and specifically acts upon and binds to
the AAA(+) domain of the PspF transcription activator.
Length = 220
Score = 29.7 bits (67), Expect = 1.6
Identities = 29/111 (26%), Positives = 52/111 (46%), Gaps = 7/111 (6%)
Query: 64 RYRSLQEPMQIRRDNLEDALLL-YQYL-RDVDDEMQWLLEKEPLAVSTDLGNSLTAVQSL 121
+ +E + + AL + L R+ E+ LEK+ A+ T L +AV+ L
Sbjct: 59 KLEEQKEQAKKLENKARAALTKGNEELAREALAEIA-TLEKQAEALETQLTQQRSAVEQL 117
Query: 122 QKKHQALETELASREPVVSALASRAK----QMSRSAHFAAARIEGATSALQ 168
+K+ ALET++ + +AL +R K Q + + +A E AT + +
Sbjct: 118 RKQLAALETKIQQLKAKKTALKARLKAAKAQEAVNTSLGSASTESATDSFE 168
>gnl|CDD|215066 PLN00125, PLN00125, Succinyl-CoA ligase [GDP-forming] subunit
alpha.
Length = 300
Score = 29.6 bits (66), Expect = 2.1
Identities = 15/47 (31%), Positives = 22/47 (46%)
Query: 131 ELASREPVVSALASRAKQMSRSAHFAAARIEGATSALQDKLASLRNA 177
E + +PVV+ +A R A A + G QDK+ +LR A
Sbjct: 229 ESGTEKPVVAFIAGLTAPPGRRMGHAGAIVSGGKGTAQDKIKALREA 275
>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional.
Length = 1047
Score = 29.8 bits (67), Expect = 2.2
Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 10/81 (12%)
Query: 63 HRYRSLQEPMQIRRDNLEDALLLYQY-LRDVDDEMQWLLEKEPLAVSTDLGNSLTAVQSL 121
+ Q+ ++ R+ L AL Y L D+E WL ++ A S Q
Sbjct: 630 QQIIQYQQQIEQRQQQLLTALAGYALTLPQEDEEASWLATRQQEAQSW---------QQR 680
Query: 122 QKKHQALETELASREPVVSAL 142
Q + AL+ + P++ L
Sbjct: 681 QNELTALQNRIQQLTPLLETL 701
>gnl|CDD|235995 PRK07338, PRK07338, hypothetical protein; Provisional.
Length = 402
Score = 28.8 bits (65), Expect = 3.8
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 140 SALASRAKQMSRSAHFAAARIEGATSALQDK 170
+A A RA R+A AAA + A AL +
Sbjct: 214 AAHAGRAFDEGRNAIVAAAELALALHALNGQ 244
>gnl|CDD|130078 TIGR01005, eps_transp_fam, exopolysaccharide transport protein
family. The model describes the exopolysaccharide
transport protein family in bacteria. The transport
protein is part of a large genetic locus which is
associated with exopolysaccharide (EPS) biosynthesis.
Detailed molecular characterization and gene fusion
analysis revealed atleast seven gene products are
involved in the overall regulation, which among other
things, include exopolysaccharide biosynthesis, property
of conferring virulence and exopolysaccharide export
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 754
Score = 28.4 bits (63), Expect = 5.3
Identities = 19/115 (16%), Positives = 40/115 (34%), Gaps = 15/115 (13%)
Query: 76 RDNLEDALLLYQYLR------DVDDEMQWLLEKEPLAVSTDLGNSLTAVQSLQKKHQALE 129
+ L + D+ M L P V+ + +++ L + ++
Sbjct: 285 KLEDLIQRLRERQAELRATIADLSTTM---LANHPRVVA-----AKSSLADLDAQIRSEL 336
Query: 130 TELASREPVVSALA-SRAKQMSRSAHFAAARIEGATSALQDKLASLRNAASVRRL 183
++ + + A +R Q+ + A A D A R+AA+ R+L
Sbjct: 337 QKITKSLLMQADAAQARESQLVSDVNQLKAASAQAGEQQVDLDALQRDAAAKRQL 391
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 28.0 bits (63), Expect = 6.1
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 111 LGNSLTAVQSLQKKHQALETELASREPVVSALASRA----------KQMSRSAHFAAARI 160
L SL+A ++ + + QAL ELA +A RA KQ+S A +
Sbjct: 86 LRASLSAAEAERSRLQALLAELAGAG---AAAEGRAGELAQELDSEKQVSARALAQVELL 142
Query: 161 EGATSALQDKLASLRNA 177
+AL+ +LA+L A
Sbjct: 143 NQQIAALRRQLAALEAA 159
>gnl|CDD|235877 PRK06850, PRK06850, hypothetical protein; Provisional.
Length = 507
Score = 28.0 bits (63), Expect = 6.4
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 12/72 (16%)
Query: 239 PILHSSDFGRDEDSVLS-----------LIKKLESLERELVSFQHTVGHLSKLCQSLLDR 287
P S FG DE +L L++KL LER+ G KL + +L +
Sbjct: 404 PGDDQSLFGSDEADLLEELCQEDGLHLELVRKLLDLERQYRGLSRRSGIYDKL-EKILKQ 462
Query: 288 NHFDSKNISKKQ 299
+ + I++
Sbjct: 463 DWRSLEEIAQNA 474
>gnl|CDD|238773 cd01515, Arch_FBPase_1, Archaeal fructose-1,6-bisphosphatase and
related enzymes of inositol monophosphatase family
(FBPase class IV). These are Mg++ dependent
phosphatases. Members in this family may have both
fructose-1,6-bisphosphatase and inositol-monophosphatase
activity. In hyperthermophilic archaea, inositol
monophosphatase is thought to play a role in the
biosynthesis of di-myo-inositol-1,1'-phosphate, an
osmolyte unique to hyperthermophiles.
Length = 257
Score = 27.7 bits (62), Expect = 6.9
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 180 VRRLRLLDALESQMLYLASGYLE 202
VRR+R+ ++ ++ Y+ASG L+
Sbjct: 172 VRRVRIFGSVALELCYVASGALD 194
>gnl|CDD|198374 cd07808, FGGY_D-XK_EcXK-like, Escherichia coli xylulokinase-like
D-xylulose kinases; a subgroup of the FGGY family of
carbohydrate kinases. This subgroup is predominantly
composed of bacterial D-xylulose kinases (XK, also known
as xylulokinase; EC 2.7.1.17), which catalyze the
rate-limiting step in the ATP-dependent phosphorylation
of D-xylulose to produce D-xylulose 5-phosphate (X5P)
and ADP. D-xylulose has been used as a source of carbon
and energy by a variety of microorganisms. Some
uncharacterized sequences are also included in this
subgroup. The prototypical member of this CD is
Escherichia coli xylulokinase (EcXK), which exists as a
dimer. Each monomer consists of two large domains
separated by an open cleft that forms an active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain. The presence of Mg2+ or Mn2+
is required for catalytic activity. Members of this
subgroup belong to the FGGY family of carbohydrate
kinases.
Length = 482
Score = 27.8 bits (63), Expect = 8.0
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 153 AHFAAARIEGATSALQDKLASLRNA-ASVRRLRL 185
AH A +EG +L+D L LR + R+
Sbjct: 364 AHLTRAVLEGVAFSLRDSLEILRELGVPIDRIIA 397
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 0.131 0.365
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,924,188
Number of extensions: 1419241
Number of successful extensions: 1557
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1550
Number of HSP's successfully gapped: 57
Length of query: 303
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 207
Effective length of database: 6,679,618
Effective search space: 1382680926
Effective search space used: 1382680926
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 (21.8 bits)
S2: 59 (26.5 bits)