RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4245
(328 letters)
>gnl|CDD|190534 pfam03131, bZIP_Maf, bZIP Maf transcription factor. Maf
transcription factors contain a conserved basic region
leucine zipper (bZIP) domain, which mediates their
dimerisation and DNA binding property. Thus, this family
is probably related to pfam00170.
Length = 93
Score = 127 bits (322), Expect = 4e-37
Identities = 46/89 (51%), Positives = 66/89 (74%)
Query: 224 ISDDLLMCLSVRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTN 283
SDD L+ +SVRELN+ L G ++++ +LK +RRTLKNRGYAQ+CRSKR+ QR ELE
Sbjct: 1 FSDDQLVSMSVRELNRHLRGLSKEEVIRLKQRRRTLKNRGYAQSCRSKRVQQRHELEKEK 60
Query: 284 KHLQQQLQKMKSEIKQIVEERNHYKKQYE 312
LQQQ++++K E+ ++ ER+ K +YE
Sbjct: 61 SQLQQQVEQLKQEVSRLARERDALKAKYE 89
>gnl|CDD|197664 smart00338, BRLZ, basic region leucin zipper.
Length = 65
Score = 55.3 bits (134), Expect = 3e-10
Identities = 17/61 (27%), Positives = 34/61 (55%)
Query: 252 LKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQY 311
K +RR +NR A+ R ++ + +ELE + L+ + +++K EI+++ E K +
Sbjct: 4 EKRRRRRERNREAARRSRERKKAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63
Query: 312 E 312
E
Sbjct: 64 E 64
>gnl|CDD|201054 pfam00170, bZIP_1, bZIP transcription factor. The Pfam entry
includes the basic region and the leucine zipper region.
Length = 64
Score = 36.1 bits (84), Expect = 0.001
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 250 AKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKK 309
+LK +RR KNR A+ R ++ E L+++++++++E K + E KK
Sbjct: 2 KELKRERRRQKNREAARRSRLRKK-AYIE------ELEEKVKELEAENKTLRSELERLKK 54
Query: 310 QYE 312
+
Sbjct: 55 ECA 57
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 38.8 bits (91), Expect = 0.003
Identities = 17/83 (20%), Positives = 42/83 (50%), Gaps = 2/83 (2%)
Query: 236 ELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKS 295
EL ++L +++ K+K + L + Q ++ Q ++L T + L ++L++++
Sbjct: 338 ELEEELKEL-EEELEKIKKLLKKLPKKARGQL-PPEKREQLEKLLETKEKLSEELEELEE 395
Query: 296 EIKQIVEERNHYKKQYEIVMRNK 318
E+K++ EE + +I +
Sbjct: 396 ELKELKEELESLYSEGKISVNKT 418
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 36.8 bits (86), Expect = 0.006
Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 7/84 (8%)
Query: 230 MCLSVRELNKKLHGYPRDQIAKLKAKRRTLKN-RGYAQNCRSKRLHQRQELEVTNKHLQQ 288
+ + +L K+L + +IA+L+A+ LK R + R++ L + ++LE K L+
Sbjct: 67 LKTRLEKLKKELEEL-KQRIAELQAQIEKLKKGREETEE-RTELLEELKQLEKELKKLKA 124
Query: 289 QLQKMKS----EIKQIVEERNHYK 308
+L+K + I+++ EE K
Sbjct: 125 ELEKYEKNDPERIEKLKEETKVAK 148
>gnl|CDD|192773 pfam11559, ADIP, Afadin- and alpha -actinin-Binding. This family
is found in mammals where it is localised at cell-cell
adherens junctions, and in Sch. pombe and other fungi
where it anchors spindle-pole bodies to spindle
microtubules. It is a coiled-coil structure, and in
pombe, it is required for anchoring the minus end of
spindle microtubules to the centrosome equivalent, the
spindle-pole body. The name ADIP derives from the family
being composed of Afadin- and alpha -Actinin-Binding
Proteins Localised at Cell-Cell Adherens Junctions.
Length = 149
Score = 36.5 bits (85), Expect = 0.006
Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 12/91 (13%)
Query: 235 RELNKKLHGYPRDQ--IAKLKAKRRTLKNR--GYAQNCRSKRLHQRQELEVTNKHLQQQL 290
L K R Q I +LK + L+ R + LE K+ ++++
Sbjct: 57 ETLRKLEAEIERLQNTIERLKTQLEDLERELALLQAKERQLEKKLK-TLEQKLKNEKEEV 115
Query: 291 QKMKSEIKQIVEERNHYKKQYEIVMRNKDRS 321
Q++K+ I+Q K QY ++ +DR
Sbjct: 116 QRLKNIIQQR-------KTQYNHELKKRDRE 139
>gnl|CDD|163064 TIGR02894, DNA_bind_RsfA, transcription factor, RsfA family. In a
subset of endospore-forming members of the Firmcutes,
members of this protein family are found, several to a
genome. Two very strongly conserved sequences regions
are separated by a highly variable linker region. Much
of the linker region was excised from the seed alignment
for this model. A characterized member is the
prespore-specific transcription RsfA from Bacillus
subtilis, previously called YwfN, which is controlled by
sigma factor F and seems to fine-tune expression of some
genes in the sigma-F regulon. A paralog in Bacillus
subtilis is designated YlbO [Regulatory functions, DNA
interactions, Cellular processes, Sporulation and
germination].
Length = 161
Score = 35.9 bits (83), Expect = 0.012
Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 247 DQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNH 306
D I+ L+ + T + Q + +Q + L+ N+ L+++L+K++ +EE
Sbjct: 84 DVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQR-LSTIEE--- 139
Query: 307 YKKQYEIVMRNKDR 320
Y+ ++ DR
Sbjct: 140 ---DYQTLIDIMDR 150
>gnl|CDD|203738 pfam07716, bZIP_2, Basic region leucine zipper.
Length = 54
Score = 33.4 bits (77), Expect = 0.013
Identities = 11/47 (23%), Positives = 27/47 (57%)
Query: 253 KAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQ 299
+ + R +N A+ R K+ + +ELE K L+++ +++ +++Q
Sbjct: 4 EYRDRRRRNNEAARRSREKKKQREEELEERVKELEEENAQLRQKVEQ 50
>gnl|CDD|221494 pfam12257, DUF3608, Protein of unknown function (DUF3608). This
domain family is found in eukaryotes, and is
approximately 280 amino acids in length. The family is
found in association with pfam00610.
Length = 281
Score = 35.1 bits (81), Expect = 0.041
Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 12/77 (15%)
Query: 32 FEDVNVKREIINNNEQDATNHNISNHQRLPSIQS--IPVPNGGSVHIQSP---------- 79
E N KR+++ N + ++ + LP I+S + N + + P
Sbjct: 170 KEFANFKRDLMLNKTSEDKGKSVIRGRFLPVIKSNILEAINLATTLVNDPFRQTDLKHTN 229
Query: 80 PHHLLTPPGSSIHPQDY 96
H ++ PG+ ++ DY
Sbjct: 230 THVIIITPGTGLYDVDY 246
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 35.1 bits (81), Expect = 0.049
Identities = 14/83 (16%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERN 305
++I +L+ K L+ + + ++ELE L+ + ++++ E+K++ EE+
Sbjct: 834 EEEIEELEEKLDELEEE--LEELEKELEELKEELE----ELEAEKEELEDELKELEEEKE 887
Query: 306 HYKKQYEIVMRNKDRSEAEHLYL 328
+++ + + E L
Sbjct: 888 ELEEELRELESELAELKEEIEKL 910
Score = 33.1 bits (76), Expect = 0.20
Identities = 18/95 (18%), Positives = 46/95 (48%), Gaps = 8/95 (8%)
Query: 234 VRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRL----HQRQELEVTNKHLQQQ 289
++EL K+L +++++L+ + L+ K + + +EL + LQ++
Sbjct: 234 LKELRKELEEL-EEELSRLEEELEELQEE---LEEAEKEIEELKSELEELREELEELQEE 289
Query: 290 LQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAE 324
L ++K EI+++ E + +++ E + + E
Sbjct: 290 LLELKEEIEELEGEISLLRERLEELENELEELEER 324
Score = 32.0 bits (73), Expect = 0.50
Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 11/85 (12%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERN 305
R+++A+L+A+ ++N + + LE + L ++L+ +K E+K++ E
Sbjct: 382 REELAELEAELAEIRNELEELK------REIESLEERLERLSERLEDLKEELKELEAELE 435
Query: 306 HYKKQY-----EIVMRNKDRSEAEH 325
+ + E+ + E
Sbjct: 436 ELQTELEELNEELEELEEQLEELRD 460
Score = 30.1 bits (68), Expect = 1.8
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 5/82 (6%)
Query: 248 QIAKLKAKRRTLKNRGYAQNCRSKRLHQ--RQELEVTNKH---LQQQLQKMKSEIKQIVE 302
+A+L+ + L+ + A + L + R+EL ++ +L+++K EI+ + E
Sbjct: 352 LLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEE 411
Query: 303 ERNHYKKQYEIVMRNKDRSEAE 324
++ E + EAE
Sbjct: 412 RLERLSERLEDLKEELKELEAE 433
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 35.1 bits (81), Expect = 0.053
Identities = 23/107 (21%), Positives = 26/107 (24%), Gaps = 12/107 (11%)
Query: 58 QRLPSIQSIPVPNGGSVHIQSPPHHLLTPPGSSIHPQDYQNSMLHGGVLMYPGTPGTPPD 117
R + P + Q P H P Q P P P
Sbjct: 186 PRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPA------QPPLPPQLPQQ 239
Query: 118 TPPGSNSPPHQHYHHMD--HPSHPHIQQLPPRAQTYHDMFMPPHPNP 162
PP M P P QQ PP+ Q PP P
Sbjct: 240 PPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQ----AQPPPQNQP 282
Score = 32.0 bits (73), Expect = 0.46
Identities = 22/106 (20%), Positives = 27/106 (25%), Gaps = 6/106 (5%)
Query: 61 PSIQSIPVPNGGSVHIQSPPHHLLTPPGS-----SIHPQDYQNSMLHGGVLMYPGTPGTP 115
+P P + PP P +PQ Q + P
Sbjct: 167 QQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQA 226
Query: 116 PDTPPGSNSPPHQHYHHMDHPSHPHIQQLPPRA-QTYHDMFMPPHP 160
P PP P Q QQ+PP Q PP P
Sbjct: 227 PAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQP 272
>gnl|CDD|191114 pfam04859, DUF641, Plant protein of unknown function (DUF641).
Plant protein of unknown function.
Length = 132
Score = 33.1 bits (76), Expect = 0.060
Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 18/88 (20%)
Query: 249 IAKLKA----KRRTLKNRGYAQNCRSKRLHQRQEL-------EVTNKHLQQQLQKMKSEI 297
+A+LK KRR + R + + QE E+ K L+ +++ SEI
Sbjct: 52 VAELKKLSELKRRYRRKRQKGAPQDAILAAEIQEQRSLLKTYEIMVKKLEAEVRAKDSEI 111
Query: 298 KQIVEERNHYKKQYEIVMRNKDRSEAEH 325
+ E K E+++ N + E
Sbjct: 112 DSLRE------KLEELLVANS-KLEKRL 132
>gnl|CDD|193537 cd05661, M28_like_PA_2, M28 Zn-Peptidases containing a PA domain
insert. Peptidase family M28 (also called
aminopeptidase Y family), uncharacterized subfamily. The
M28 family contains aminopeptidases as well as
carboxypeptidases. They have co-catalytic zinc ions;
each zinc ion is tetrahedrally co-ordinated, with three
amino acid ligands plus activated water; one aspartate
residue binds both metal ions. This subfamily is
composed of uncharacterized proteins containing a
protease-associated (PA) domain insert which may
participate in substrate binding and/or promote
conformational changes, influencing the stability and
accessibility of the site to substrate.
Length = 305
Score = 34.5 bits (80), Expect = 0.061
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 8/48 (16%)
Query: 2 RVRAPNTIAMVDSEDPQLADEYVQEFVLD-HFEDVNVKREI----INN 44
V +PN + ++ DP L DEYV VL H + + + + I N
Sbjct: 63 DVTSPNVVGVLPGSDPALKDEYV---VLSAHLDHIGIGEPVGGDNIYN 107
>gnl|CDD|222417 pfam13851, GAS, Growth-arrest specific micro-tubule binding. This
family is the highly conserved central region of a
number of metazoan proteins referred to as growth-arrest
proteins. In mouse, Gas8 is predominantly a testicular
protein, whose expression is developmentally regulated
during puberty and spermatogenesis. In humans, it is
absent in infertile males who lack the ability to
generate gametes. The localisation of Gas8 in the
motility apparatus of post-meiotic gametocytes and
mature spermatozoa, together with the detection of Gas8
also in cilia at the apical surfaces of epithelial cells
lining the pulmonary bronchi and Fallopian tubes
suggests that the Gas8 protein may have a role in the
functioning of motile cellular appendages. Gas8 is a
microtubule-binding protein localised to regions of
dynein regulation in mammalian cells.
Length = 201
Score = 33.4 bits (77), Expect = 0.092
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 18/79 (22%)
Query: 234 VRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKM 293
V EL KKL Y K K + LK R +ELE K+L+ + + +
Sbjct: 71 VEELRKKLKDY-----EKDKQSLKNLKAR-------------LKELEKELKNLKWESEVL 112
Query: 294 KSEIKQIVEERNHYKKQYE 312
+ +++ ER+ ++E
Sbjct: 113 EQRFEKVERERDELYDKFE 131
Score = 30.3 bits (69), Expect = 0.90
Identities = 16/79 (20%), Positives = 36/79 (45%), Gaps = 11/79 (13%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRL-----HQRQELEVTNKHLQQ------QLQKMK 294
+++IA++K + +KRL +E+E K L+ L+ +K
Sbjct: 33 KEEIAEMKKNEEHNEKLMAEIAQENKRLVEPLKKAEEEVEELRKKLKDYEKDKQSLKNLK 92
Query: 295 SEIKQIVEERNHYKKQYEI 313
+ +K++ +E + K + E+
Sbjct: 93 ARLKELEKELKNLKWESEV 111
>gnl|CDD|206034 pfam13863, DUF4200, Domain of unknown function (DUF4200). This
family is found in eukaryotes. It is a coiled-coil
domain of unknwon function.
Length = 126
Score = 32.2 bits (74), Expect = 0.11
Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 250 AKLKAKRRTLKNR-----GYAQNCRSKR----------LHQRQELEVTNKHLQQQLQKMK 294
+L+ K L+ + + +KR R+E E K L+ +L+++K
Sbjct: 35 EELEKKEEELQESLIKFDKFLKENEAKRRRAEKKAEEEKKLRKEKEEEIKELKAELEELK 94
Query: 295 SEIKQIVEERNHYKKQYEIVM 315
+EI+++ E+ Y+ YE +
Sbjct: 95 AEIEKLEEKLEEYQP-YEEFL 114
Score = 29.9 bits (68), Expect = 0.81
Identities = 9/44 (20%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 271 KRLHQRQELEVTNKHLQQQLQKMKSEIKQIVE-ERNHYKKQYEI 313
+ L +R+E+E L + ++ + + + + E KK+ E+
Sbjct: 1 RLLEKRREMEEVQLALDAKREEFERREELLKQREEELEKKEEEL 44
Score = 29.5 bits (67), Expect = 1.1
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 250 AKLKAKRRTLKNRGYAQNCRSKRLHQRQ-ELEVTNKHLQQQLQKMKSEIKQIVEERNHYK 308
L AKR + R + L QR+ ELE + LQ+ L K +K+ +R +
Sbjct: 14 LALDAKREEFERR-------EELLKQREEELEKKEEELQESLIKFDKFLKENEAKRRRAE 66
Query: 309 KQYEIVMRNKDRSEAE 324
K+ E + + E E
Sbjct: 67 KKAEEEKKLRKEKEEE 82
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 34.2 bits (79), Expect = 0.11
Identities = 24/92 (26%), Positives = 46/92 (50%), Gaps = 13/92 (14%)
Query: 234 VRELNKKLH--GYPRDQ--IAKLKAKRRTLKNRGYAQNCRSKR--LHQ---RQELEVTNK 284
++EL ++L G P D + +A+R L R RS+R L + E E+ N
Sbjct: 1036 LQELKQELQDLGVPADSGAEERARARRDELHAR--LSANRSRRNQLEKQLTFCEAEMDN- 1092
Query: 285 HLQQQLQKMKSEIKQIVEERNHYKKQYEIVMR 316
L ++L+K++ + ++ E+ + K + V+R
Sbjct: 1093 -LTKKLRKLERDYHEMREQVVNAKAGWCAVLR 1123
>gnl|CDD|227796 COG5509, COG5509, Uncharacterized small protein containing a
coiled-coil domain [Function unknown].
Length = 65
Score = 31.0 bits (70), Expect = 0.11
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 224 ISDDLLMCLSVRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRL 273
I +D L LSV EL +++ + +I +LKA+ K A +RL
Sbjct: 17 IGNDALSLLSVAELEERI-ALLQAEIERLKAELAKKKASRSAAEALFRRL 65
>gnl|CDD|153369 cd07685, F-BAR_Fes, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma)
tyrosine kinase. F-BAR domains are dimerization modules
that bind and bend membranes and are found in proteins
involved in membrane dynamics and actin reorganization.
Fes (feline sarcoma), also called Fps (Fujinami poultry
sarcoma), is a cytoplasmic (or nonreceptor) tyrosine
kinase whose gene was first isolated from tumor-causing
retroviruses. It is expressed in myeloid, vascular
endothelial, epithelial, and neuronal cells, and plays
important roles in cell growth and differentiation,
angiogenesis, inflammation and immunity, and
cytoskeletal regulation. Fes kinase has also been
implicated as a tumor suppressor in colorectal cancer.
It contains an N-terminal F-BAR domain, an SH2 domain,
and a C-terminal catalytic kinase domain. F-BAR domains
form banana-shaped dimers with a positively-charged
concave surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules. The F-BAR domain of Fes is
critical in its role in microtubule nucleation and
bundling.
Length = 237
Score = 33.0 bits (75), Expect = 0.16
Identities = 12/42 (28%), Positives = 28/42 (66%)
Query: 287 QQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAEHLYL 328
QQ ++K+KS+ + + ++ K++Y+ ++KDR +A+ Y+
Sbjct: 130 QQDIEKLKSQYRSLAKDSAQAKRKYQEASKDKDRDKAKEKYV 171
>gnl|CDD|130214 TIGR01144, ATP_synt_b, ATP synthase, F0 subunit b. This model
describes the F1/F0 ATP synthase b subunit in bacteria
only. Scoring just below the trusted cutoff are the
N-terminal domains of Mycobacterial b/delta fusion
proteins and a subunit from an archaeon, Methanosarcina
barkeri, in which the ATP synthase homolog differs in
architecture and is not experimentally confirmed. This
model helps resolve b from the related b' subunit.
Within the family is an example from a
sodium-translocating rather than proton-translocating
ATP synthase [Energy metabolism, ATP-proton motive force
interconversion].
Length = 147
Score = 32.0 bits (73), Expect = 0.16
Identities = 12/51 (23%), Positives = 24/51 (47%)
Query: 276 RQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAEHL 326
++E + K Q L++ K E ++I+E N + + + R E E +
Sbjct: 42 KKEAALAQKKAQVILKEAKDEAQEIIENANKRGSEILEEAKAEAREEREKI 92
>gnl|CDD|148614 pfam07106, TBPIP, Tat binding protein 1(TBP-1)-interacting protein
(TBPIP). This family consists of several eukaryotic
TBP-1 interacting protein (TBPIP) sequences. TBP-1 has
been demonstrated to interact with the human
immunodeficiency virus type 1 (HIV-1) viral protein Tat,
then modulate the essential replication process of HIV.
In addition, TBP-1 has been shown to be a component of
the 26S proteasome, a basic multiprotein complex that
degrades ubiquitinated proteins in an ATP-dependent
fashion. Human TBPIP interacts with human TBP-1 then
modulates the inhibitory action of human TBP-1 on
HIV-Tat-mediated transactivation.
Length = 169
Score = 32.3 bits (74), Expect = 0.17
Identities = 25/106 (23%), Positives = 48/106 (45%), Gaps = 26/106 (24%)
Query: 223 LISDDLLMCLSVRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQ-ELEV 281
L + D S ELNK +I +L+ + + LK Q+C + + + ++
Sbjct: 60 LCNQDQFELPSDEELNKL-----DMEIEELREEVQLLK-----QDCSTLEIELKSLTSDL 109
Query: 282 TNKHLQQQLQKMKSEIKQI---------------VEERNHYKKQYE 312
T + LQ+++Q++K E+++I EE KK+Y+
Sbjct: 110 TTEELQEEIQELKKEVREIEEKLESLEEGWKPVTPEEMEKVKKEYK 155
>gnl|CDD|129204 TIGR00096, TIGR00096, probable S-adenosylmethionine-dependent
methyltransferase, YraL family. No member of this
family is characterized, but pfam00590 (tetrapyrrole
methylase) demonstrates homology between this family
and its other members, which include several methylases
for the tetrapyrrole class of compound, as well as the
enzyme diphthine synthase [Unknown function, Enzymes of
unknown specificity].
Length = 276
Score = 32.5 bits (74), Expect = 0.23
Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 3/56 (5%)
Query: 29 LDHFEDVNVKREIINNNEQDATNHNISNHQRLPSIQSIPVPNGGSVHIQSPPHHLL 84
L K I+N Q+ N+ +L +I V + + S P HLL
Sbjct: 41 LHLGIIATPKAFHIDNEFQEKQ--NLLA-AKLEIGNNIAVSSDAGPPLISDPGHLL 93
>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 = 33.1 bits (76), Expect = 0.24
Identities = 23/102 (22%), Positives = 49/102 (48%), Gaps = 13/102 (12%)
Query: 233 SVRELNKKLH------GYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLH----QRQELEVT 282
+RE+ +KL+ Y +I +L+ +R LK + K + +++ELE
Sbjct: 813 RLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQ---IKSIEKEIENLNGKKEELEEE 869
Query: 283 NKHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAE 324
+ L+ L+ ++S + + +ER+ + Q + R + EA+
Sbjct: 870 LEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQ 911
Score = 29.3 bits (66), Expect = 4.0
Identities = 19/93 (20%), Positives = 49/93 (52%), Gaps = 2/93 (2%)
Query: 233 SVRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQR-QELEVTNKHLQQQLQ 291
++ L ++L G R +++ L+++ R ++NR + ++ E+E + L+Q+ +
Sbjct: 675 ELQRLRERLEGLKR-ELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEE 733
Query: 292 KMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAE 324
K+K ++++ E+ + +++ E V EA
Sbjct: 734 KLKERLEELEEDLSSLEQEIENVKSELKELEAR 766
Score = 28.9 bits (65), Expect = 5.1
Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 13/78 (16%)
Query: 235 RELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMK 294
ELNKK+ ++ ++K K L+ + LE + +++L+ +
Sbjct: 275 EELNKKIKDLGEEEQLRVKEKIGELEA-------------EIASLERSIAEKERELEDAE 321
Query: 295 SEIKQIVEERNHYKKQYE 312
+ ++ E + + E
Sbjct: 322 ERLAKLEAEIDKLLAEIE 339
Score = 28.1 bits (63), Expect = 7.7
Identities = 14/82 (17%), Positives = 34/82 (41%), Gaps = 15/82 (18%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQ---------------ELEVTNKHLQQQL 290
R+++ KLK + LK +RL + ELE + ++
Sbjct: 391 REKLEKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEI 450
Query: 291 QKMKSEIKQIVEERNHYKKQYE 312
+K + +++Q+ + + Y+++
Sbjct: 451 KKQEWKLEQLAADLSKYEQELY 472
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 32.8 bits (75), Expect = 0.24
Identities = 15/93 (16%), Positives = 42/93 (45%), Gaps = 8/93 (8%)
Query: 235 RELNKKLHGYPR---DQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQ-ELEVTNKHLQQQL 290
EL +L + + + + R L+ + +RL + + E+E L+++L
Sbjct: 252 EELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEELEREIEE----LEEEL 307
Query: 291 QKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEA 323
+ +++ ++++ E K E + + +++ E
Sbjct: 308 EGLRALLEELEELLEKLKSLEERLEKLEEKLEK 340
Score = 32.8 bits (75), Expect = 0.28
Identities = 27/125 (21%), Positives = 48/125 (38%), Gaps = 25/125 (20%)
Query: 218 YSESDLISDDLLMCLSVRELNKKLHGYPRDQIAKLKAKRRTLKN--RGYAQNCRSKRLHQ 275
+E + ++L L L +L + + +L+ K L+ R Q R+
Sbjct: 625 ENELEEAEEELESELEKLNLQAELEELLQAALEELEEKVEELEAEIRRELQ-----RIEN 679
Query: 276 RQELEVTNKHLQQQ-------------LQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSE 322
++LE + L+Q L K EI+Q++EE K + E + + E
Sbjct: 680 EEQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEELESRKAELE-----ELKKE 734
Query: 323 AEHLY 327
E L
Sbjct: 735 LEKLE 739
Score = 32.4 bits (74), Expect = 0.41
Identities = 24/119 (20%), Positives = 48/119 (40%), Gaps = 15/119 (12%)
Query: 219 SESDLISDDLLMCLSVRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQE 278
E I D+L +L++ L ++ I + KAK L+ + + L + E
Sbjct: 154 KERKEILDELFGLEKYEKLSELL----KEVIKEAKAKIEELEGQLSELLEDIEDLLEALE 209
Query: 279 LEVTNKH------LQQQLQKMKSEIKQI---VEERNHYKKQYEIVMRNKDRSEAEHLYL 328
E+ +Q+ ++++ EI+ + + E K++ E + E E L L
Sbjct: 210 EELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEEL--KARLLEIESLEL 266
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 32.4 bits (75), Expect = 0.31
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 9/73 (12%)
Query: 234 VRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRL-HQRQELEVTNKHLQQQLQK 292
+RE +L + +L K L + R + L + +ELE QQ+L+K
Sbjct: 77 LRERRNEL----QKLEKRLLQKEENLDRKLELLEKREEELEKKEKELE----QKQQELEK 128
Query: 293 MKSEIKQIVEERN 305
+ E+++++EE+
Sbjct: 129 KEEELEELIEEQL 141
Score = 30.1 bits (69), Expect = 1.5
Identities = 18/93 (19%), Positives = 41/93 (44%), Gaps = 10/93 (10%)
Query: 234 VRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKM 293
+ E +++H + +L+ +R L+ KRL Q++E + K + L+K
Sbjct: 59 LLEAKEEIHKLRNEFEKELRERRNELQKL-------EKRLLQKEEN-LDRK--LELLEKR 108
Query: 294 KSEIKQIVEERNHYKKQYEIVMRNKDRSEAEHL 326
+ E+++ +E +++ E + E L
Sbjct: 109 EEELEKKEKELEQKQQELEKKEEELEELIEEQL 141
>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 = 32.7 bits (75), Expect = 0.33
Identities = 15/80 (18%), Positives = 35/80 (43%), Gaps = 7/80 (8%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEE-R 304
R ++ +L + R L+++ RS+ + +EL L+ +L+ ++ I + E
Sbjct: 893 RSELEELSEELRELESK------RSELRRELEELREKLAQLELRLEGLEVRIDNLQERLS 946
Query: 305 NHYKKQYEIVMRNKDRSEAE 324
Y E +++ E +
Sbjct: 947 EEYSLTLEEAEALENKIEDD 966
Score = 29.6 bits (67), Expect = 2.6
Identities = 19/91 (20%), Positives = 40/91 (43%), Gaps = 2/91 (2%)
Query: 234 VRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKM 293
+ L K+ QIA L + L+ R R +RL Q E + +L+++
Sbjct: 381 LETLRSKVAQ-LELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKLEE-AELKEL 438
Query: 294 KSEIKQIVEERNHYKKQYEIVMRNKDRSEAE 324
++E++++ EE +++ E + + E
Sbjct: 439 QAELEELEEELEELQEELERLEEALEELREE 469
Score = 28.9 bits (65), Expect = 5.2
Identities = 19/96 (19%), Positives = 46/96 (47%), Gaps = 6/96 (6%)
Query: 232 LSVRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSK--RL-HQRQELEVTNKHLQQ 288
L + EL ++L ++++ + + + L Q K L + ELE + LQ+
Sbjct: 232 LRLEELREELEEL-QEELKEAEEELEELTAE--LQELEEKLEELRLEVSELEEEIEELQK 288
Query: 289 QLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAE 324
+L + +EI ++ +++ +++ + R + EA+
Sbjct: 289 ELYALANEISRLEQQKQILRERLANLERQLEELEAQ 324
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 32.1 bits (74), Expect = 0.41
Identities = 13/55 (23%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 249 IAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEE 303
IA L+ R L+ + A+ + +E E + L+++ +K++ E +++EE
Sbjct: 522 IASLEELERELEQK--AEEAEALL----KEAEKLKEELEEKKEKLQEEEDKLLEE 570
Score = 31.0 bits (71), Expect = 0.89
Identities = 13/71 (18%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 247 DQIAKLKAKRRTLKNRGYAQNCRSKRLHQ-RQELEVTNKHLQQQLQKMKSEIK--QIVEE 303
++ KL+ + L A+ + + + ++E + K L+Q + + +K +++E
Sbjct: 555 EKKEKLQEEEDKLLEE--AEKEAQQAIKEAKKEADEIIKELRQLQKGGYASVKAHELIEA 612
Query: 304 RNHYKKQYEIV 314
R K E
Sbjct: 613 RKRLNKANEKK 623
>gnl|CDD|113545 pfam04778, LMP, LMP repeated region. This family consists of a
repeated sequence element found in the LMP group of
surface-located membrane proteins of Mycoplasma hominis.
The the number of repeats in the protein affects the
tendency of cells to spontaneously aggregate.
Agglutination may be an important factor in
colonisation. Non-agglutinating microorganisms might
easily be distributed whereas aggregation might provide
a better chance to avoid an antibody response since some
of the epitopes may be buried.
Length = 157
Score = 31.0 bits (70), Expect = 0.41
Identities = 26/101 (25%), Positives = 42/101 (41%), Gaps = 22/101 (21%)
Query: 234 VRELNKKLHGYPRDQIAKLKAKRRTLK-----------NRGYA---QNCRSKRLHQ---- 275
V E+ KKL + +D+ AK K +T K N Y+ ++ SK+ +
Sbjct: 53 VTEITKKLETFNKDKDAKFKELEQTRKDIDEFINTNKNNPNYSTLVKDLTSKKDSKNSVT 112
Query: 276 ----RQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYE 312
+ ++E N L+Q L K K+ QI K+Q
Sbjct: 113 NSSNKSDIEAANTELKQALAKAKAAKDQIDNANKSIKEQLN 153
>gnl|CDD|221404 pfam12067, Sox_C_TAD, Sox C-terminal transactivation domain. This
domain is found at the C-terminus of the Sox family of
transcription factors. It is found associated with
pfam00505. It binds to the Armadillo repeats (pfam00514)
in Catenin beta-1 (CTNNB1), which is involved in
transcriptional regulation. It functions as a
transactivating domain (TAD).
Length = 197
Score = 31.2 bits (71), Expect = 0.48
Identities = 20/87 (22%), Positives = 30/87 (34%), Gaps = 8/87 (9%)
Query: 73 SVHIQSPPHHLLTPPGSSIHPQDYQNSMLHGGV-LMYPGTPGTPPDTPPGSNSPPHQHYH 131
S Q + SS PQ+ L + + G+P + G +PP +Y
Sbjct: 41 SPPCQEDCQMMPYGYNSSYAPQNAHAPALLRQMAVTENIPQGSPAPSIMGCPTPPQMYYG 100
Query: 132 HMDHPSHP-----HIQQL--PPRAQTY 151
M P + QL PP +Q
Sbjct: 101 QMYVPECAKHHPVQLGQLSPPPESQHL 127
>gnl|CDD|234342 TIGR03752, conj_TIGR03752, integrating conjugative element protein,
PFL_4705 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida toluene catabolic TOL plasmid pWWO_p085. Usually,
however, they are found on the bacterial main chromosome
in regions flanked by markers of conjugative transfer
and/or transposition [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 472
Score = 31.9 bits (73), Expect = 0.49
Identities = 18/93 (19%), Positives = 43/93 (46%), Gaps = 10/93 (10%)
Query: 233 SVRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQR--QELEVTNKHLQQQL 290
V+EL K+L + LKA+ L+ R + + Q+ Q ++ + L +++
Sbjct: 67 EVKELRKRLAKL-ISENEALKAENERLQKR-------EQSIDQQIQQAVQSETQELTKEI 118
Query: 291 QKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEA 323
+++KSE +Q+ + +++ V+ +
Sbjct: 119 EQLKSERQQLQGLIDQLQRRLAGVLTGPSGGGS 151
>gnl|CDD|203371 pfam06005, DUF904, Protein of unknown function (DUF904). This
family consists of several bacterial and archaeal
hypothetical proteins of unknown function.
Length = 72
Score = 29.2 bits (66), Expect = 0.50
Identities = 12/56 (21%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 247 DQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVE 302
+ IA L+ + LK + + +ELE NK L+++ +S ++ ++
Sbjct: 18 ETIALLQMEIEELKEENEQLS------EENEELEEENKKLKEERNAWQSRLRALLG 67
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 31.8 bits (73), Expect = 0.52
Identities = 18/91 (19%), Positives = 38/91 (41%), Gaps = 25/91 (27%)
Query: 234 VRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQE--------------- 278
+ E +++H + +LK +R L+ +RL QR+E
Sbjct: 53 LLEAKEEVHKLRAELERELKERRNELQRL-------ERRLLQREETLDRKMESLDKKEEN 105
Query: 279 LEVTNKHL---QQQLQKMKSEIKQIVEERNH 306
LE K L ++ L + + E+++++ E+
Sbjct: 106 LEKKEKELSNKEKNLDEKEEELEELIAEQRE 136
>gnl|CDD|219186 pfam06810, Phage_GP20, Phage minor structural protein GP20. This
family consists of several phage minor structural
protein GP20 sequences of around 180 residues in length.
The function of this family is unknown.
Length = 156
Score = 30.8 bits (70), Expect = 0.54
Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 233 SVRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQK 292
+ K P+ ++ K +R +LK + +N R K++ ++ N+ LQ++++K
Sbjct: 6 KIMAEYGKDIQNPKSKLDKANEERDSLKKQ--LKN-RDKQIEDLKKKVKDNEELQKKIEK 62
Query: 293 MKSEIKQIVEERNHYKKQY 311
+K + K EE Y+ +
Sbjct: 63 LKQQNKTAKEE---YEAKL 78
>gnl|CDD|224259 COG1340, COG1340, Uncharacterized archaeal coiled-coil protein
[Function unknown].
Length = 294
Score = 31.2 bits (71), Expect = 0.57
Identities = 20/90 (22%), Positives = 36/90 (40%), Gaps = 18/90 (20%)
Query: 235 RELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMK 294
ELN K+ R++ +L+ +R + Q + KR N LQ+ +
Sbjct: 44 DELNAKVREL-REKAQELREERDEINEE--VQELKEKRDE-------INAKLQELRK--- 90
Query: 295 SEIKQIVEERNHYKKQYEIVMRNKDRSEAE 324
E +++ E+RN + R+ E E
Sbjct: 91 -EYRELKEKRNEFNL----GGRSIKSLERE 115
Score = 29.3 bits (66), Expect = 2.6
Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 7/77 (9%)
Query: 236 ELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKS 295
EL +K R + ++L KR L + + + QEL + +++Q++K
Sbjct: 24 ELKEKRDEL-RKEASELAEKRDELNAK------VRELREKAQELREERDEINEEVQELKE 76
Query: 296 EIKQIVEERNHYKKQYE 312
+ +I + +K+Y
Sbjct: 77 KRDEINAKLQELRKEYR 93
Score = 28.9 bits (65), Expect = 3.5
Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 11/82 (13%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERN 305
+++I +LK KR L+ A KR ++ + L+++ Q+++ E +I EE
Sbjct: 19 KEEIEELKEKRDELRKE--ASELAEKRDELNAKV----RELREKAQELREERDEINEEVQ 72
Query: 306 HYKKQYEIVMRNKDRSEAEHLY 327
K++ R++ ++ + L
Sbjct: 73 ELKEK-----RDEINAKLQELR 89
Score = 27.7 bits (62), Expect = 8.6
Identities = 14/74 (18%), Positives = 30/74 (40%), Gaps = 8/74 (10%)
Query: 236 ELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKS 295
EL K+L + + K + LK + K +++ + L + Q+
Sbjct: 142 ELRKELED--AKKALEENEKLKELKAE--IDELKKKAREIHEKI----QELANEAQEYHE 193
Query: 296 EIKQIVEERNHYKK 309
E+ ++ EE + +K
Sbjct: 194 EMIKLFEEADELRK 207
>gnl|CDD|149160 pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein. The sequences
featured in this family are similar to a region of human
TPR protein and to yeast myosin-like proteins 1 (MLP1)
and 2 (MLP2). These proteins share a number of features;
for example, they all have coiled-coil regions and all
three are associated with nuclear pores. TPR is thought
to be a component of nuclear pore complex- attached
intra-nuclear filaments, and is implicated in nuclear
protein import. Moreover, its N-terminal region is
involved in the activation of oncogenic kinases,
possibly by mediating the dimerisation of kinase domains
or by targeting these kinases to the nuclear pore
complex. MLP1 and MLP2 are involved in the process of
telomere length regulation, where they are thought to
interact with proteins such as Tel1p and modulate their
activity.
Length = 132
Score = 30.3 bits (69), Expect = 0.59
Identities = 14/80 (17%), Positives = 33/80 (41%), Gaps = 3/80 (3%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKH--LQQQLQKMKSEIKQIVEE 303
++ + K + L+ Q + Q+ E E+ KH ++LQ ++ ++ ++ +E
Sbjct: 16 LEKKEDAEEKIQKLQEDLEEQAEIANEAQQKYERELV-KHAEDIEELQALRKQLNELKKE 74
Query: 304 RNHYKKQYEIVMRNKDRSEA 323
K + E +E
Sbjct: 75 IAQLKAEAESAQAELSEAEE 94
>gnl|CDD|219358 pfam07271, Cytadhesin_P30, Cytadhesin P30/P32. This family
consists of several Mycoplasma species specific
Cytadhesin P32 and P30 proteins. P30 has been found to
be membrane associated and localised on the tip
organelle. It is thought that it is important in
cytadherence and virulence.
Length = 279
Score = 30.8 bits (69), Expect = 0.76
Identities = 29/127 (22%), Positives = 36/127 (28%), Gaps = 9/127 (7%)
Query: 46 EQDATNHNISNHQRLPSIQSIPVPNGGSVHIQ-SPPHHLLTPPGSSIHPQDYQNSMLHGG 104
E D T + P+ ++ V Q P P P M G
Sbjct: 129 EIDPTEEVNTQEPTQPAGVNVANNPQPQVQPQFGPNPQQRINPQRFGFPMQPNMGMRPGF 188
Query: 105 VLMYPGTPGTPPDTP-PGSNSPPHQHYHHMDHPSHPHIQQLPPRAQTYHDMFMPPHPNPF 163
M P PG PP+ PG N P P P Q P + P P F
Sbjct: 189 NQMPPHMPGMPPNQMRPGFNPMPGM-------PPRPGFNQNPNMMPNMNRPGFRPQPGGF 241
Query: 164 RQEEVPL 170
P+
Sbjct: 242 NHPGTPM 248
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 30.8 bits (70), Expect = 0.89
Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 14/91 (15%)
Query: 235 RELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMK 294
LN ++I LKA + L R++ ++ EL + Q K+
Sbjct: 153 GALNPAR----AERIDALKATLKQLAAV------RAEIAAEQAELTTLLSEQRAQQAKLA 202
Query: 295 SEIKQIVEERNHYKKQYEIVMRNKDRSEAEH 325
Q++EER Q + + E
Sbjct: 203 ----QLLEERKKTLAQLNSELSADQKKLEEL 229
>gnl|CDD|180240 PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated.
Length = 156
Score = 30.1 bits (69), Expect = 0.89
Identities = 12/53 (22%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 276 RQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYEIV--MRNKDRSEAEHL 326
++ELE+ + QL + ++E +I+E+ K+ +I+ + + +EA +
Sbjct: 51 KKELELAQAKYEAQLAEARAEAAEIIEQAK--KRAAQIIEEAKAEAEAEAARI 101
>gnl|CDD|227889 COG5602, SIN3, Histone deacetylase complex, SIN3 component
[Chromatin structure and dynamics].
Length = 1163
Score = 31.0 bits (70), Expect = 0.97
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 3/62 (4%)
Query: 65 SIPVPNGGSVHIQSPPHHLLTPPGSSIHPQDYQNSMLHGGVLMYPGTPGTPPDTPPGSNS 124
S+P PNG +H+ +P L +PP S + N H +P P P +
Sbjct: 200 SLPQPNGSRLHVTTPQGPLSSPPVQSSYYVAPCN---HDQRTSHPTLPSDSQPEPSAPSH 256
Query: 125 PP 126
P
Sbjct: 257 MP 258
>gnl|CDD|153370 cd07686, F-BAR_Fer, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Fer (Fes related)
tyrosine kinase. F-BAR domains are dimerization modules
that bind and bend membranes and are found in proteins
involved in membrane dynamics and actin reorganization.
Fer (Fes related) is a cytoplasmic (or nonreceptor)
tyrosine kinase expressed in a wide variety of tissues,
and is found to reside in both the cytoplasm and the
nucleus. It plays important roles in neuronal
polarization and neurite development, cytoskeletal
reorganization, cell migration, growth factor signaling,
and the regulation of cell-cell interactions mediated by
adherens junctions and focal adhesions. Fer kinase also
regulates cell cycle progression in malignant cells. It
contains an N-terminal F-BAR domain, an SH2 domain, and
a C-terminal catalytic kinase domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 234
Score = 30.4 bits (68), Expect = 1.0
Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 273 LHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQY-EIVMRNKDRSEAEHLY 327
+HQ+ E E+ K + +L+K+K +Q+ +E N K++Y + V + K+ +A Y
Sbjct: 113 VHQQIEAEM-YKVTKTELEKLKCSYRQLTKEVNSAKEKYKDAVAKGKETEKARERY 167
Score = 27.3 bits (60), Expect = 9.9
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSE----IKQIV 301
R++ K K L N+ Y + +LHQ Q + T L LQKM+ E +K I+
Sbjct: 164 RERYDKATMKLHMLHNQ-YVLAVKGAQLHQHQYYDFTLPLLLDSLQKMQEEMIKALKGIL 222
Query: 302 EE 303
+E
Sbjct: 223 DE 224
>gnl|CDD|114855 pfam06160, EzrA, Septation ring formation regulator, EzrA. During
the bacterial cell cycle, the tubulin-like cell-division
protein FtsZ polymerises into a ring structure that
establishes the location of the nascent division site.
EzrA modulates the frequency and position of FtsZ ring
formation.
Length = 559
Score = 30.6 bits (70), Expect = 1.2
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 284 KHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAEHL 326
K +++ L ++ +I+QI+EE N K+ E K+R E E L
Sbjct: 104 KEIEELLDTIEEDIEQILEELNELKESEE-----KNRKEVEEL 141
>gnl|CDD|149849 pfam08912, Rho_Binding, Rho Binding. Rho Binding Domain is
responsible for the recognition and binding of Rho
binding domain-containing proteins (such as ROCK) to
Rho, resulting in activation of the GTPase which in turn
modulates the phosphorylation of various signalling
proteins. This domain is within an amphipathic
alpha-helical coiled-coil and interacts with Rho through
predominantly hydrophobic interactions.
Length = 68
Score = 28.2 bits (63), Expect = 1.2
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 280 EVTN--KHLQQQLQKMKSEIKQIVEERNHYKKQ 310
E+ N K Q++LQK+K E + I + ++KQ
Sbjct: 13 ELNNKLKKAQEELQKLKEEEQSINNIKAAFEKQ 45
>gnl|CDD|221408 pfam12072, DUF3552, Domain of unknown function (DUF3552). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria, archaea and eukaryotes.
This domain is about 200 amino acids in length. This
domain is found associated with pfam00013, pfam01966.
This domain has a single completely conserved residue A
that may be functionally important.
Length = 201
Score = 29.8 bits (68), Expect = 1.3
Identities = 25/94 (26%), Positives = 42/94 (44%), Gaps = 30/94 (31%)
Query: 232 LSVRELNKKLHGYPRDQIAK-LKAKRRTLKNRGYAQNCRSKRLHQRQE------------ 278
L +E KL R + + LK +R L+ + KRL Q++E
Sbjct: 56 LEAKEEIHKL----RAEAERELKERRNELQRQ-------EKRLLQKEETLDRKDESLEKK 104
Query: 279 ---LEVTNKHL---QQQLQKMKSEIKQIVEERNH 306
LE K L QQQL++ + E+++++EE+
Sbjct: 105 EESLEEKEKELAARQQQLEEKEEELEELIEEQQQ 138
>gnl|CDD|219690 pfam07996, T4SS, Type IV secretion system proteins. Members of
this family are components of the type IV secretion
system. They mediate intracellular transfer of
macromolecules via a mechanism ancestrally related to
that of bacterial conjugation machineries.
Length = 195
Score = 30.0 bits (68), Expect = 1.3
Identities = 7/35 (20%), Positives = 17/35 (48%)
Query: 288 QQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSE 322
QQL + ++ Q+ ++ K+QY + ++
Sbjct: 19 QQLAQWAQQLDQLKQQIQQAKQQYNSITGSRGLGA 53
>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family. This family of
proteins contain a band 4.1 domain (pfam00373), at their
amino terminus. This family represents the rest of these
proteins.
Length = 244
Score = 30.1 bits (68), Expect = 1.5
Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 14/76 (18%)
Query: 235 RELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMK 294
R K+L Y +L+ K + + + Q LE L+++ ++++
Sbjct: 22 RRAQKELEEYEE-TALELEEKLKQEE-------------EEAQLLEKKADELEEENRRLE 67
Query: 295 SEIKQIVEERNHYKKQ 310
E EER + +
Sbjct: 68 EEAAASEEERERLEAE 83
Score = 28.6 bits (64), Expect = 3.8
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 276 RQELEVTNKHLQQQLQKMKSEIKQIVEERN--HYKKQYEIVMR 316
R N+ LQ QLQ +KSE+ +E +E +R
Sbjct: 175 RVTYAEKNERLQTQLQALKSELAAARDESKETANDILHEENVR 217
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 30.2 bits (69), Expect = 1.5
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 284 KHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAEHL 326
++ L ++ +I+QI+EE + E K+R E E L
Sbjct: 108 NEIESLLDLIEEDIEQILEELQELLESEE-----KNREEVEQL 145
>gnl|CDD|227657 COG5354, COG5354, Uncharacterized protein, contains Trp-Asp (WD)
repeat [General function prediction only].
Length = 561
Score = 30.2 bits (68), Expect = 1.7
Identities = 26/114 (22%), Positives = 51/114 (44%), Gaps = 11/114 (9%)
Query: 194 EPSRPMSVSSSSVMSPSSRTTTCPYSESDLISDDLLM---CLSVRELNKKLHGY-PRDQI 249
EP +++ S+ SR P+ ++ ++ D +EL ++ Y D+I
Sbjct: 455 EPPSKLTIESAKKYVKPSRHRFVPFEKAVIMEADSANRSSAPRKKELVEQWPEYSDEDKI 514
Query: 250 AKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEE 303
L K R A +R+ +ELEV + + +++ SE+K++VE+
Sbjct: 515 RSLLKKLR-------AIEALKERMRSGEELEVIQVNKIETEEEVLSELKELVED 561
>gnl|CDD|217754 pfam03836, RasGAP_C, RasGAP C-terminus.
Length = 139
Score = 29.1 bits (66), Expect = 1.7
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 19/76 (25%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVT-------NKHLQQQLQKMKSEIK 298
+ IA ++N+ + R K + ++LE T NK+L+ QL KS +
Sbjct: 32 LNDIAN------DIRNKRRYRERRKK---ELKKLEQTLKKLRDKNKYLESQLDYYKSYLD 82
Query: 299 QIVEE---RNHYKKQY 311
++ + + KQ
Sbjct: 83 NVLSTLQKKKKFSKQK 98
>gnl|CDD|220173 pfam09311, Rab5-bind, Rabaptin-like protein. Members of this
family are predominantly found in Rabaptin and allow for
binding to the GTPase Rab5. This interaction is
necessary and sufficient for Rab5-dependent recruitment
of Rabaptin5 to early endosomal membranes.
Length = 180
Score = 29.3 bits (66), Expect = 1.8
Identities = 12/67 (17%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 246 RDQIAKLKAKRRTL--KNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEE 303
R Q+ +L+ + + L + Q ++ + +L KHLQ + + E+ +
Sbjct: 28 RAQLRRLQQENQWLRGELALTQQELQASE-QEVIQLPEEVKHLQFLCLQRREELIESRTA 86
Query: 304 RNHYKKQ 310
H +++
Sbjct: 87 SEHLEEE 93
>gnl|CDD|191511 pfam06409, NPIP, Nuclear pore complex interacting protein (NPIP).
This family consists of a series of primate specific
nuclear pore complex interacting protein (NPIP)
sequences. The function of this family is unknown but is
well conserved from African apes to humans.
Length = 350
Score = 29.8 bits (66), Expect = 2.0
Identities = 27/102 (26%), Positives = 37/102 (36%), Gaps = 4/102 (3%)
Query: 50 TNHNISNHQRLPSIQSIPVPNGGSVHIQSPPHHLLTPPGSSIHPQDYQNSMLHGGVLMYP 109
T N HQ P Q + + S+ +++PP LLTP S P N L+ P
Sbjct: 238 TLKNRMGHQPPPPTQQHSIIDN-SLSLKTPPECLLTPLPPSALPSADDNLKTPAECLLRP 296
Query: 110 GTPG---TPPDTPPGSNSPPHQHYHHMDHPSHPHIQQLPPRA 148
P + P PP D+ + LPP A
Sbjct: 297 LPPSADDNIKECPLALKPPPPLPPSVDDNLKECLLAPLPPSA 338
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 30.0 bits (68), Expect = 2.0
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQ--ELEVTNKHLQQQLQKMKSEIK-QIVE 302
R + +L+ ++++LK++ K+ + Q +L+ K L +Q Q +K E
Sbjct: 655 RLDLQRLQNEQQSLKDKLELAIAERKQQAETQLRQLDAQLKQLLEQQQAFLEALKDDFRE 714
Query: 303 ERNHYKKQYEIVMRNKDRSEAE 324
R ++++V D A+
Sbjct: 715 LRTERLAKWQVVEGELDNQLAQ 736
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 28.7 bits (65), Expect = 2.0
Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 276 RQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAE 324
+++LE K Q +L+K++ E++++ E+ +K + R + E
Sbjct: 20 QKQLEKEFKKRQAELEKLEKELQKLKEK---LQKD-AATLSEAAREKKE 64
>gnl|CDD|145995 pfam03148, Tektin, Tektin family. Tektins are cytoskeletal
proteins. They have been demonstrated in such cellular
sites as centrioles, basal bodies, and along ciliary and
flagellar doublet microtubules. Tektins form unique
protofilaments, organised as longitudinal polymers of
tektin heterodimers with axial periodicity matching
tubulin. Tektin polypeptides consist of several
alpha-helical regions that are predicted to form coiled
coils. Indeed, tektins share considerable structural
similarities with intermediate filament proteins.
Possible functional roles for tektins are: stabilisation
of tubulin protofilaments; attachment of A and B-tubules
in ciliary/flagellar microtubule doublets and C-tubules
in centrioles; binding of axonemal components.
Length = 384
Score = 29.9 bits (68), Expect = 2.1
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 11/83 (13%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQN---CRSK---RLHQR-QELEVTNKHLQQQLQKMKSEIK 298
RD+ LK + L+NR N CR + RL +ELE T L+++L + ++ +K
Sbjct: 289 RDKEGPLKVAQTRLENRTQRPNVELCRDQAQYRLIDEVKELEDTIAALKEKLAEAEASLK 348
Query: 299 QIVEERNHYKKQYEIVMRNKDRS 321
+ E + + +I K S
Sbjct: 349 AL--EETRARLEEDI--AIKANS 367
Score = 28.3 bits (64), Expect = 5.8
Identities = 15/66 (22%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRS-----KRLHQR-QELEVTNKHLQQQLQKMKSEIKQ 299
RD +L+ + R L N A + K+L +R ++ L ++L+++ +EI+
Sbjct: 16 RDLAERLRHESRRLINETDATTKWTQADVTKKLGERISDINFWKSELDRELEELIAEIEA 75
Query: 300 IVEERN 305
++E +
Sbjct: 76 LLEYKR 81
>gnl|CDD|153294 cd07610, FCH_F-BAR, The Extended FES-CIP4 Homology (FCH) or F-BAR
(FCH and Bin/Amphiphysin/Rvs) domain, a dimerization
module that binds and bends membranes. F-BAR domains
are dimerization modules that bind and bend membranes
and are found in proteins involved in membrane dynamics
and actin reorganization. F-BAR domain containing
proteins, also known as Pombe Cdc15 homology (PCH)
family proteins, include Fes and Fer tyrosine kinases,
PACSINs/Syndapins, FCHO, PSTPIP, CIP4-like proteins and
srGAPs. Many members also contain an SH3 domain and play
roles in endocytosis. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
These tubules have diameters larger than those observed
with N-BARs. The F-BAR domains of some members such as
NOSTRIN and Rgd1 are important for the subcellular
localization of the protein.
Length = 191
Score = 29.2 bits (66), Expect = 2.2
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 4/69 (5%)
Query: 262 RGYAQNCRSKRLHQRQELEVTNKHLQ----QQLQKMKSEIKQIVEERNHYKKQYEIVMRN 317
++ R + E E K LQ + +K E ++ VE+ N + +YE N
Sbjct: 89 EKVKEDKEQARKKELAEGEKLKKKLQELWAKLAKKADEEYREQVEKLNPAQSEYEEEKLN 148
Query: 318 KDRSEAEHL 326
K ++E E
Sbjct: 149 KIQAEQERE 157
>gnl|CDD|236686 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 29.7 bits (68), Expect = 2.2
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 7/37 (18%)
Query: 272 RLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYK 308
RLH +L ++L+K+K IK+ + H
Sbjct: 207 RLH-------NKTNLMEELKKIKRVIKKADPDAPHEV 236
>gnl|CDD|222579 pfam14179, YppG, YppG-like protein. The YppG-like protein family
includes the B. subtilis YppG protein, which is
functionally uncharacterized. This family of proteins is
found in bacteria. Proteins in this family are typically
between 115 and 181 amino acids in length. There are two
completely conserved residues (F and G) that may be
functionally important.
Length = 110
Score = 28.1 bits (63), Expect = 2.2
Identities = 12/49 (24%), Positives = 15/49 (30%)
Query: 114 TPPDTPPGSNSPPHQHYHHMDHPSHPHIQQLPPRAQTYHDMFMPPHPNP 162
+ P N + H P PP+ Q H M P P P
Sbjct: 5 QNTNQYPPQNQQQQPYQQQPYHQQMPPPPYSPPQQQQGHFMPPQPQPYP 53
>gnl|CDD|199882 cd02851, E_set_GO_C, C-terminal Early set domain associated with
the catalytic domain of galactose oxidase. E or
"early" set domains are associated with the catalytic
domain of galactose oxidase at the C-terminal end.
Galactose oxidase is an extracellular monomeric enzyme
which catalyzes the stereospecific oxidation of a broad
range of primary alcohol substrates and possesses a
unique mononuclear copper site essential for catalyzing
a two-electron transfer reaction during the oxidation
of primary alcohols to corresponding aldehydes. The
second redox active center necessary for the reaction
was found to be situated at a tyrosine residue. The
C-terminal domain of galactose oxidase may be related
to the immunoglobulin and/or fibronectin type III
superfamilies. These domains are associated with
different types of catalytic domains at either the
N-terminal or C-terminal end and may be involved in
homodimeric/tetrameric/dodecameric interactions.
Members of this family include members of the alpha
amylase family, sialidase, galactose oxidase,
cellulase, cellulose, hyaluronate lyase, chitobiase,
and chitinase, among others.
Length = 103
Score = 28.0 bits (63), Expect = 2.2
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 49 ATNHNISNHQRLPSIQSIPVPNGGSVHIQSPPHHLLTPPG 88
H+ + QRL + +V + +PP+ + PPG
Sbjct: 43 FVTHSFNMGQRLVKLPVTGSGGDYTVTVTAPPNANVAPPG 82
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 29.4 bits (67), Expect = 2.4
Identities = 11/50 (22%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 277 QELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAEHL 326
+ LE N L++Q+++++ +++ + E ++ E+ + +SE E L
Sbjct: 4 EALEERNSELEEQIRQLELKLRDLEAENEKLER--EL---ERLKSELEKL 48
>gnl|CDD|220213 pfam09377, SBDS_C, SBDS protein C-terminal domain. This family is
highly conserved in species ranging from archaea to
vertebrates and plants. The family contains several
Shwachman-Bodian-Diamond syndrome (SBDS) proteins from
both mouse and humans. Shwachman-Diamond syndrome is an
autosomal recessive disorder with clinical features that
include pancreatic exocrine insufficiency,
haematological dysfunction and skeletal abnormalities.
Members of this family play a role in RNA metabolism.
Length = 126
Score = 28.4 bits (64), Expect = 2.4
Identities = 11/44 (25%), Positives = 19/44 (43%)
Query: 271 KRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYEIV 314
R R + V K ++ +K+K + VEE +E+V
Sbjct: 65 ARAKMRVRVTVPVKAAKKVKEKLKKLYEFKVEEEEESGGGWELV 108
>gnl|CDD|221767 pfam12776, Myb_DNA-bind_3, Myb/SANT-like DNA-binding domain. This
presumed domain appears to be related to other Myb/SANT
like DNA binding domains. In particular pfam10545 seems
most related. This family is greatly expanded in plants
and appears in several proteins annotated as transposon
proteins.
Length = 96
Score = 27.6 bits (62), Expect = 2.7
Identities = 11/61 (18%), Positives = 24/61 (39%), Gaps = 3/61 (4%)
Query: 247 DQIAK-LKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERN 305
+Q+ + + G+ K+ +Q+ L+ T L+ + +K E + E N
Sbjct: 16 EQVDAGNRPGQGGFTKEGW--KNIVKKFNQKTGLKYTKDQLKNRWDTLKKEYRLWKELLN 73
Query: 306 H 306
Sbjct: 74 A 74
>gnl|CDD|225044 COG2133, COG2133, Glucose/sorbosone dehydrogenases [Carbohydrate
transport and metabolism].
Length = 399
Score = 29.3 bits (66), Expect = 2.8
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 1/55 (1%)
Query: 70 NGGSVHIQSPPHHLLTPPGSSIHPQDYQNSMLHGGVLMYPGTPGTPPDTPPGSNS 124
GG + P L GS+ P Q+++ G ++ G P P NS
Sbjct: 178 FGGRLVF-GPDGKLYVTTGSNGDPALAQDNVSLAGKVLRIDRAGIIPADNPFPNS 231
>gnl|CDD|215915 pfam00429, TLV_coat, ENV polyprotein (coat polyprotein).
Length = 560
Score = 29.4 bits (66), Expect = 2.8
Identities = 16/78 (20%), Positives = 21/78 (26%), Gaps = 9/78 (11%)
Query: 100 MLHGGVLMYPGTPGTPPDTPPGSNSPPHQHYHHMDHPSHPHIQQLPPR-AQTYHDMFMPP 158
L GG + P TPP + + D P P R ++ P
Sbjct: 42 DLAGGGQVSWSPPCTPPQSVCSGCPDLSAYL--TDQSLWPPCVTPPKRTPHANGSFYVCP 99
Query: 159 HPNPFRQEEVPLDMRRHC 176
RRHC
Sbjct: 100 GECR------TRANRRHC 111
>gnl|CDD|234084 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
protein, PEP-CTERM locus subfamily. Members of this
protein family belong to the family of polysaccharide
chain length determinant proteins (pfam02706). All are
found in species that encode the PEP-CTERM/exosortase
system predicted to act in protein sorting in a number
of Gram-negative bacteria, and are found near the epsH
homolog that is the putative exosortase gene [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 498
Score = 29.2 bits (66), Expect = 2.9
Identities = 11/58 (18%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 265 AQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSE 322
+ R L R E + L + + ++++E+ Q+ + K YE ++ ++ +E
Sbjct: 328 SLEARVAELTARIE---RLESLLRTIPEVEAELTQLNRDYEVNKSNYEQLLTRRESAE 382
>gnl|CDD|214016 cd12923, iSH2_PI3K_IA_R, Inter-Src homology 2 (iSH2) helical domain
of Class IA Phosphoinositide 3-kinase Regulatory
subunits. PI3Ks catalyze the transfer of the
gamma-phosphoryl group from ATP to the 3-hydroxyl of the
inositol ring of D-myo-phosphatidylinositol (PtdIns) or
its derivatives. They play an important role in a
variety of fundamental cellular processes, including
cell motility, the Ras pathway, vesicle trafficking and
secretion, immune cell activation, and apoptosis. They
are classified according to their substrate specificity,
regulation, and domain structure. Class IA PI3Ks are
heterodimers of a p110 catalytic (C) subunit and a
p85-related regulatory (R) subunit. The R subunit
down-regulates PI3K basal activity, stabilizes the C
subunit, and plays a role in the activation downstream
of tyrosine kinases. All R subunits contain two SH2
domains that flank an intervening helical domain (iSH2),
which binds to the N-terminal adaptor-binding domain
(ABD) of the catalytic subunit. In vertebrates, there
are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode
for different Class IA PI3K R subunits.
Length = 152
Score = 28.3 bits (64), Expect = 3.0
Identities = 10/67 (14%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 244 YPRDQIAKLKAKRRTLKNR-GYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVE 302
+ +L LK+R + + + ++ N+ L++++ +K E+ Q+ +
Sbjct: 69 AQPHEKQRLMENNELLKSRLKELEESKEQLEEDLRKQVAYNRELEREMNSLKPELMQLRK 128
Query: 303 ERNHYKK 309
+++ Y +
Sbjct: 129 QKDQYLR 135
>gnl|CDD|106256 PRK13296, PRK13296, tRNA CCA-pyrophosphorylase; Provisional.
Length = 360
Score = 29.2 bits (65), Expect = 3.1
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 276 RQELEVTNKHLQQQLQKMKSEIKQIVEERN 305
R+EL +TNKH + L K I +I+E+R+
Sbjct: 251 RKELLLTNKHYK--LLKASIAISKILEDRS 278
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 29.3 bits (66), Expect = 3.1
Identities = 19/92 (20%), Positives = 37/92 (40%), Gaps = 16/92 (17%)
Query: 235 RELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMK 294
RE R+ ++R K + LE N L+++L+++K
Sbjct: 404 REKEGTEEEERREITVY---EKRIKKLEE-----------TVERLEEENSELKRELEELK 449
Query: 295 SEIKQIVEERNHYKKQYEIVMRNKDRSEAEHL 326
EI+++ E ++++ +R KDR E
Sbjct: 450 REIEKLESELERFRREVRDKVR-KDR-EIRAR 479
Score = 29.3 bits (66), Expect = 3.7
Identities = 12/85 (14%), Positives = 39/85 (45%), Gaps = 4/85 (4%)
Query: 234 VRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKM 293
EL ++L + +I KL+++ + + + + + R + L+++L++
Sbjct: 438 NSELKRELEEL-KREIEKLESELERFRREVRDKVRKDREIRARDR---RIERLEKELEEK 493
Query: 294 KSEIKQIVEERNHYKKQYEIVMRNK 318
K ++++ + +K ++ + K
Sbjct: 494 KKRVEELERKLAELRKMRKLELSGK 518
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 29.2 bits (66), Expect = 3.2
Identities = 18/90 (20%), Positives = 43/90 (47%), Gaps = 16/90 (17%)
Query: 248 QIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTN-------KHLQQQLQKMKSEIKQI 300
I +AK + R Q++E ++ +H++Q ++KM++E +++
Sbjct: 205 AIEAERAKAEAAE-----AEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKL 259
Query: 301 VEERN----HYKKQYEIVMRNKDRSEAEHL 326
+ E+ H ++ E +++ ++EAE L
Sbjct: 260 LAEQERMLEHKLQEQEELLKEGFKTEAESL 289
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 28.4 bits (64), Expect = 3.4
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 276 RQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAE 324
+++LE K LQ +LQK + E+++ ++ +KQ + + R +
Sbjct: 37 QKQLEKEFKKLQAELQKKEKELQKEEQK---LQKQAAT-LSEEARKAKQ 81
>gnl|CDD|217020 pfam02403, Seryl_tRNA_N, Seryl-tRNA synthetase N-terminal domain.
This domain is found associated with the Pfam tRNA
synthetase class II domain (pfam00587) and represents
the N-terminal domain of seryl-tRNA synthetase.
Length = 108
Score = 27.6 bits (62), Expect = 3.4
Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 11/72 (15%)
Query: 247 DQIAKLKAKRRTLKNRG----YAQNCRSKRLHQ-------RQELEVTNKHLQQQLQKMKS 295
D++ +L +RR L+ +N SK + + + L K L+ +L+ +++
Sbjct: 29 DELLELDEERRELQVELEELQAERNELSKEIGKAKKKKEDAEALIAEVKELKDELKALEA 88
Query: 296 EIKQIVEERNHY 307
E++++ E +
Sbjct: 89 ELRELEAELDKL 100
>gnl|CDD|220404 pfam09789, DUF2353, Uncharacterized coiled-coil protein (DUF2353).
Members of this family of uncharacterized proteins have
no known function.
Length = 319
Score = 29.1 bits (65), Expect = 3.6
Identities = 14/65 (21%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERN 305
R IA+ + + R + R+ + Q ++L K L+ L+ + E ++++ ER+
Sbjct: 106 RQTIAQQRVEFMGGGVRESFEE-RNDLVSQLEKLREKCKQLESDLRSLLDEKEEVLMERD 164
Query: 306 HYKKQ 310
Y+++
Sbjct: 165 EYQRK 169
>gnl|CDD|226400 COG3883, COG3883, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 28.9 bits (65), Expect = 3.6
Identities = 10/40 (25%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 275 QRQELEVTNKHLQQQLQKMKSEIKQ----IVEERNHYKKQ 310
+ EL+ + +++K++ EI + IVE + KK+
Sbjct: 67 KIDELQKEIDQSKAEIKKLQKEIAELKENIVERQELLKKR 106
>gnl|CDD|234016 TIGR02791, VirB5, P-type DNA transfer protein VirB5. The VirB5
protein is involved in the type IV DNA secretion systems
typified by the Agrobacterium Ti plasmid vir system
where it interacts with several other proteins essential
for proper pilus formation. VirB5 is homologous to the
IncN (N-type) conjugation system protein TraC as well as
the P-type protein TrbJ and the F-type protein TraE.
Length = 220
Score = 28.7 bits (64), Expect = 4.0
Identities = 9/33 (27%), Positives = 20/33 (60%)
Query: 287 QQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKD 319
+Q+ +K++ +Q+ E+ YK+QY + N+
Sbjct: 40 IEQMAALKTQYEQLSEQIEQYKQQYGSLTGNRG 72
>gnl|CDD|234366 TIGR03825, FliH_bacil, flagellar assembly protein FliH. This
bacillus clade of FliH proteins is not found by the Pfam
FliH model pfam02108, but is closely related to the
sequences identified by that model. Sequences identified
by this model are observed in flagellar operons in an
analogous position relative to other flagellar operon
genes.
Length = 255
Score = 28.6 bits (64), Expect = 4.2
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 276 RQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMR--NKDRSEAEH 325
QEL + +Q L+K ++E QI+E+ Q + ++R++ E
Sbjct: 32 EQELADEEQEFEQILEKAEAEAAQIIEQAE---AQAAAIREQIEQERAQWEE 80
>gnl|CDD|218651 pfam05600, DUF773, Protein of unknown function (DUF773). This
family contains several eukaryotic sequences which are
thought to be CDK5 activator-binding proteins, however,
the function of this family is unknown.
Length = 506
Score = 28.9 bits (65), Expect = 4.3
Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 27/89 (30%)
Query: 234 VRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKM 293
V L +KL Q KLK KR + + RQE +++ +
Sbjct: 437 VETLEQKLK-----QEDKLKEKRELMTEK-------------RQEA-------REEQSSL 471
Query: 294 KSEIKQIVEERNHYKKQYE--IVMRNKDR 320
+ ++ ++E+ +K E I R R
Sbjct: 472 EPKLDLLIEKTRELQKLIEADISKRYNGR 500
>gnl|CDD|225638 COG3096, MukB, Uncharacterized protein involved in chromosome
partitioning [Cell division and chromosome
partitioning].
Length = 1480
Score = 29.1 bits (65), Expect = 4.4
Identities = 16/77 (20%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 247 DQIAKLKAKRRTLKNRGYAQNCRSKRL----HQRQ-------ELEVTNKHLQQQLQKMKS 295
+Q+ L+ + L+ R Q ++RL +RQ ELE ++ L+ ++ +
Sbjct: 513 EQVQPLRMRLSELEQR-LRQQQSAERLLADFCKRQGKNLDAEELEALHQELEALIESLSD 571
Query: 296 EIKQIVEERNHYKKQYE 312
+ E+R +++ E
Sbjct: 572 SVSNAREQRMALRQEQE 588
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional.
Length = 330
Score = 28.6 bits (65), Expect = 4.4
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 269 RSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKK 309
++ Q+ ELEVT +L +Q ++MK E+K + ++ K
Sbjct: 30 AQRKKSQKGELEVT--NLNEQYKEMKEELKAALLDKKELKA 68
>gnl|CDD|220105 pfam09084, NMT1, NMT1/THI5 like. This family contains the NMT1 and
THI5 proteins. These proteins are proposed to be
required for the biosynthesis of the pyrimidine moiety
of thiamine. They are regulated by thiamine.
Length = 216
Score = 28.3 bits (64), Expect = 4.4
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 6/39 (15%)
Query: 76 IQSPPHHLLTPPGSSIH-PQDYQNSMLHGGVLMYPGTPG 113
IQ PP+ L+ S I P+D L G + Y G+P
Sbjct: 70 IQHPPNGLIYLKDSGIKSPKD-----LKGKRIGYSGSPF 103
>gnl|CDD|235295 PRK04405, prsA, peptidylprolyl isomerase; Provisional.
Length = 298
Score = 28.6 bits (64), Expect = 4.5
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 283 NKHLQQQLQKMKSEIKQIVEERNHYKKQY 311
+ L++Q K K K++ ++ N YKKQY
Sbjct: 64 YRALEKQYGK-KVSTKKVDKQYNSYKKQY 91
>gnl|CDD|220411 pfam09802, Sec66, Preprotein translocase subunit Sec66. Members of
this family of proteins are a component of the
heterotetrameric Sec62/63 complex composed of SEC62,
SEC63, SEC66 and SEC72. The Sec62/63 complex associates
with the Sec61 complex to form the Sec complex. Sec 66
is involved in SRP-independent post-translational
translocation across the endoplasmic reticulum and
functions together with the Sec61 complex and KAR2 in a
channel-forming translocon complex. Furthermore, Sec66
is also required for growth at elevated temperatures.
Length = 190
Score = 28.1 bits (63), Expect = 4.5
Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 256 RRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQ---QLQKMKSEIKQIVEERNHYKK 309
RR++K + L+Q + + Q+ + M+ E+K +V+E Y+
Sbjct: 87 RRSIKLKENKPAL--NILYQNGS--IGDDLWQRFQRAEKLMELELKDVVQEAETYQP 139
>gnl|CDD|165098 PHA02730, PHA02730, ankyrin-like protein; Provisional.
Length = 672
Score = 28.8 bits (64), Expect = 4.6
Identities = 15/27 (55%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 34 DVNVKREIINNNEQDATNHNISNHQRL 60
DVNV R I+ NN A NH +SN+ RL
Sbjct: 394 DVNVVRFIVENNGHMAINH-VSNNGRL 419
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 29.0 bits (65), Expect = 4.7
Identities = 6/35 (17%), Positives = 19/35 (54%)
Query: 270 SKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEER 304
++ +++ L+ K + L++ + E+KQ+ +
Sbjct: 349 TELEKRKEALDQALKSARDALEERERELKQVRAQL 383
>gnl|CDD|132364 TIGR03321, alt_F1F0_F0_B, alternate F1F0 ATPase, F0 subunit B. A
small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, CC and in principle may run in either direction.
This model represents the F0 subunit B of this apparent
second ATP synthase.
Length = 246
Score = 28.5 bits (64), Expect = 4.7
Identities = 9/42 (21%), Positives = 20/42 (47%)
Query: 265 AQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNH 306
A + + +R+E E N+ L QQ + + ++ K+ +
Sbjct: 48 ADTKKREAEQERREYEEKNEELDQQREVLLTKAKEEAQAERQ 89
>gnl|CDD|191096 pfam04799, Fzo_mitofusin, fzo-like conserved region. Family of
putative transmembrane GTPase. The fzo protein is a
mediator of mitochondrial fusion. This conserved region
is also found in the human mitofusin protein.
Length = 171
Score = 28.1 bits (63), Expect = 4.9
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 35/92 (38%)
Query: 253 KAKRRTLKNR--GYAQ------------NCRSKRLHQ-RQEL-----------EVTNKHL 286
KAK R K + YA NC HQ +QEL +VT+K L
Sbjct: 70 KAKERAFKRQFVDYATEKLQLIVSLTSSNCS----HQVQQELASTFARLCQQVDVTSKDL 125
Query: 287 QQQLQKMKSEIKQIVEERNHYKKQYEIVMRNK 318
++++ ++ EI+++ ++ K ++RNK
Sbjct: 126 EEEIAELTKEIQRLETIQSRSK-----LLRNK 152
>gnl|CDD|227406 COG5074, COG5074, t-SNARE complex subunit, syntaxin [Intracellular
trafficking and secretion].
Length = 280
Score = 28.3 bits (63), Expect = 4.9
Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 12/63 (19%)
Query: 272 RLHQRQELEVTNKHLQQQLQKMK----------SEIKQIVEERNHYKKQYEIVMRNKDRS 321
+ +R + + NK Q + + K + EE+ ++QY I + +
Sbjct: 86 KSAERDGIHLANKQAQAENVRQKFLKLIQDYRIIDSNYREEEKEQARRQYIIA--QPEAT 143
Query: 322 EAE 324
E E
Sbjct: 144 EDE 146
>gnl|CDD|129323 TIGR00219, mreC, rod shape-determining protein MreC. MreC (murein
formation C) is involved in the rod shape determination
in E. coli, and more generally in cell shape
determination of bacteria whether or not they are
rod-shaped. Cells defective in MreC are round. Species
with MreC include many of the Proteobacteria,
Gram-positives, and spirochetes [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 283
Score = 28.3 bits (63), Expect = 4.9
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 276 RQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYE 312
RQEL N+ L+ Q +K E ++ E N E
Sbjct: 79 RQELLKKNQQLEILTQNLKQENVRLRELLNSPLSSDE 115
>gnl|CDD|233230 TIGR01000, bacteriocin_acc, bacteriocin secretion accessory
protein. This family represents an accessory protein
that works with the bacteriocin maturation and ABC
transport secretion protein described by TIGR01193
[Transport and binding proteins, Other].
Length = 457
Score = 28.5 bits (64), Expect = 5.3
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 275 QRQELEVTNKHLQQQLQKMKSEIKQIVEERNHY 307
Q+Q LE +L+ Q + + + + I RN +
Sbjct: 98 QKQLLEQQLDNLKDQKKSLDTLKQSIENGRNQF 130
>gnl|CDD|145416 pfam02252, PA28_beta, Proteasome activator pa28 beta subunit. PA28
activator complex (also known as 11s regulator of 20S
proteasome) is a ring shaped hexameric structure of
alternating alpha and beta subunits. This family
represents the beta subunit. The activator complex binds
to the 20S proteasome ana simulates peptidase activity
in and ATP-independent manner.
Length = 150
Score = 27.6 bits (62), Expect = 5.3
Identities = 8/24 (33%), Positives = 18/24 (75%)
Query: 282 TNKHLQQQLQKMKSEIKQIVEERN 305
+N+ + L+K+K EI++++E+ N
Sbjct: 7 SNEKIVALLEKVKPEIRELIEKCN 30
>gnl|CDD|220897 pfam10883, DUF2681, Protein of unknown function (DUF2681). This
family of proteins is found in bacteria. Proteins in
this family are typically between 81 and 117 amino acids
in length.
Length = 87
Score = 26.6 bits (59), Expect = 5.4
Identities = 7/42 (16%), Positives = 18/42 (42%), Gaps = 6/42 (14%)
Query: 269 RSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQ 310
+ K+ + N+ LQ + +++ +E E + K +
Sbjct: 24 KLKKAQRE------NRKLQAENEQLATEKAVAETEVKNAKVR 59
>gnl|CDD|151045 pfam10482, CtIP_N, Tumour-suppressor protein CtIP N-terminal
domain. CtIP is predominantly a nuclear protein that
complexes with both BRCA1 and the BRCA1-associated RING
domain protein (BARD1). At the protein level, CtIP
expression varies with cell cycle progression in a
pattern identical to that of BRCA1. Thus, the
steady-state levels of CtIP polypeptides, which remain
low in resting cells and G1 cycling cells, increase
dramatically as Dividing cells traverse the G1/S
boundary. CtIP can potentially modulate the functions
ascribed to BRCA1 in transcriptional regulation, DNA
repair, and/or cell cycle checkpoint control. This
N-terminal domain carries a coiled-coil region and is
essential for homodimerisation of the protein. The
C-terminal domain is family pfam08573.
Length = 120
Score = 27.5 bits (61), Expect = 5.4
Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 7/98 (7%)
Query: 221 SDLISDDLLMCLSVRELNKKLHGYPRDQIAKLKAKRRTLKNR---GYAQNCRSKRLHQR- 276
+ L + L + E K R+Q L+ R L++R G C +
Sbjct: 24 AKLKKERCLDAQRLEEFFSKNQ-QLREQQKVLQENIRVLEDRLRAGLCDRCTVTEELAKK 82
Query: 277 --QELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYE 312
QELE ++ Q + ++ +E+K + EE ++ +
Sbjct: 83 KQQELENNHQQNLQVISELTNEMKTLTEENRRLSEELK 120
>gnl|CDD|213400 cd12193, B_zip1, basic leucine zipper DNA-binding and
multimerization region of GCN4 and related proteins.
Basic leucine zipper (bZIP) transcription factors act in
networks of homo- and hetero-dimers in the regulation in
a diverse set of cellular pathways. Classical leucine
zippers have alpha helices with leucine residues 7 amino
acids apart, which stabilize dimerization with a
parallel leucine zipper domain. Dimerization creates a
pair of basic regions that bind DNA and undergo
conformational change. GCN4 was identified in
Saccharomyces cerevisiae from mutations in a deficiency
in activation with the general amino acid control
pathway. GCN4 encodes a trans-activator of amino acid
biosynthetic genes containing 2 acidic activation
domains and a C-terminal bZIP domain, comprised of a
basic alpha-helical DNA-binding region and a coiled-coil
dimerization region.
Length = 54
Score = 25.7 bits (57), Expect = 5.6
Identities = 10/54 (18%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 252 LKAKRRTLKNRGYAQNCRSKRLHQRQELE-------VTNKHLQQQLQKMKSEIK 298
R+ +NR A+ R++++ + ++LE N L+ ++ ++K +
Sbjct: 1 DPRARKRARNREAARRSRARKMERMKQLEDKVEELTSENSDLEDEVDRLKKALA 54
>gnl|CDD|220624 pfam10187, Nefa_Nip30_N, N-terminal domain of NEFA-interacting
nuclear protein NIP30. This is a the N-terminal 100
amino acids of a family of proteins conserved from
plants to humans. The full-length protein has putatively
been called NEFA-interacting nuclear protein NIP30,
however no reference could be found to confirm this.
Length = 99
Score = 27.0 bits (60), Expect = 5.9
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 275 QRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAEHL 326
E E + L ++LQ+ K + ++ EE+ K Q+ R D E E L
Sbjct: 26 AEPEEEYDGRSLYERLQENKDKKQEEFEEKFKLKNQF----RGLDEDEVEFL 73
>gnl|CDD|226193 COG3667, PcoB, Uncharacterized protein involved in copper
resistance [Inorganic ion transport and metabolism].
Length = 321
Score = 28.3 bits (63), Expect = 5.9
Identities = 23/114 (20%), Positives = 30/114 (26%), Gaps = 11/114 (9%)
Query: 72 GSVHIQSPPHHLLTPPGSSIHPQDYQNSMLHGGVLMYPGTPGTPPDTPPGSNSPPHQHYH 131
G + Q P P P D + + G M P + H
Sbjct: 18 GPLVAQPHPTEAAQPHAHEHAPMDAPHPAMPG---MDHHAHSKMPGPEMAAPQMDHGAMP 74
Query: 132 HMDHPSHPHIQQLPPRAQTYHDMFMPPHPNPFRQEEVP--LDMRRHCAADWSLV 183
HMDH P Q + P R P M+ H S+V
Sbjct: 75 HMDHAPP------PIPTQHAAERSRSPASAAARVAAFPPAQGMKEHDGGLASIV 122
>gnl|CDD|240420 PTZ00441, PTZ00441, sporozoite surface protein 2 (SSP2);
Provisional.
Length = 576
Score = 28.4 bits (63), Expect = 5.9
Identities = 32/139 (23%), Positives = 45/139 (32%), Gaps = 26/139 (18%)
Query: 33 EDVNVKREIINNNEQDATNHNISNHQRLPSIQSIPVPNGGSVHIQSPPHHLLTPPGSSIH 92
ED N R + N + +P PVP +P L PPG
Sbjct: 300 EDDN-PRPTDDEFAVPNFNEGLD----VPDNPQDPVPPPNEGKDGNPNEENLFPPGDDEV 354
Query: 93 PQDYQNSMLHGGVLMYPGTPGTPPDTPPGSNSPPHQHYHHMDHPSHPHIQQLPPRAQTYH 152
P + P PP+ P GSNS + +P +P I + P
Sbjct: 355 PDE-------------SNVPPNPPNVPGGSNSEFSSDVENPPNPPNPDIPEQEPNI---- 397
Query: 153 DMFMPPHPNPFRQEEVPLD 171
P N E+VP++
Sbjct: 398 ----PEDSNKEVPEDVPME 412
>gnl|CDD|182106 PRK09841, PRK09841, cryptic autophosphorylating protein tyrosine
kinase Etk; Provisional.
Length = 726
Score = 28.3 bits (63), Expect = 6.1
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 286 LQQQLQKMKSEIKQIVEERNHYKKQYEIV 314
LQ+QL +++SE+ Q E+ N Y++Q + V
Sbjct: 272 LQRQLPEVRSELDQAEEKLNVYRQQRDSV 300
>gnl|CDD|236458 PRK09293, PRK09293, fructose-1,6-bisphosphatase; Provisional.
Length = 327
Score = 28.3 bits (64), Expect = 6.2
Identities = 6/21 (28%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 96 YQNSMLHGGVLMYPGTPGTPP 116
++ +L GG+ +YP P
Sbjct: 245 HRI-LLKGGIFLYPADEPYPN 264
>gnl|CDD|219737 pfam08172, CASP_C, CASP C terminal. This domain is the C-terminal
region of the CASP family of proteins. It is a Golgi
membrane protein which is thought to have a role in
vesicle transport.
Length = 245
Score = 28.1 bits (63), Expect = 6.3
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 272 RLHQR-QELEVTNKHLQQQLQKMKSEIKQ 299
R +R ELE + Q + ++ E++
Sbjct: 90 RFRKRNTELEEELRKQNQTISSLRRELES 118
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 28.5 bits (63), Expect = 6.4
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 236 ELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKS 295
ELN+KL ++QI LK+K LK+ L +RQ+ E L ++Q +
Sbjct: 846 ELNRKLIQDQQEQIQHLKSKTNELKSEKLQI---GTNLQRRQQFEEQLVELSTEVQSLIR 902
Query: 296 EIKQIVEE 303
EIK E+
Sbjct: 903 EIKDAKEQ 910
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.4 bits (63), Expect = 6.5
Identities = 26/109 (23%), Positives = 32/109 (29%), Gaps = 17/109 (15%)
Query: 67 PVPNGGSVHIQSPPHHLLTPPGSSIHPQDYQNSMLHGGVLMYPGTPGTPPDTPPGSNSPP 126
P+P S +PP PPG S+ GG + +P P PP
Sbjct: 2827 PLPPPTSAQPTAPP----PPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPP 2882
Query: 127 HQHYHH-------------MDHPSHPHIQQLPPRAQTYHDMFMPPHPNP 162
+ D P P Q PP Q PP P P
Sbjct: 2883 VRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQP 2931
>gnl|CDD|223860 COG0789, SoxR, Predicted transcriptional regulators
[Transcription].
Length = 124
Score = 27.0 bits (60), Expect = 6.7
Identities = 16/92 (17%), Positives = 38/92 (41%), Gaps = 8/92 (8%)
Query: 218 YSESDLISDDLLMCLSVRELNKKLHGYPRDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQ 277
Y+ DL +LL + + G+ +I +L ++ + + +
Sbjct: 39 YTPEDL---ELLQII----KTLRELGFSLAEIKELLDLLSAGESIA-LELRERLLAERLE 90
Query: 278 ELEVTNKHLQQQLQKMKSEIKQIVEERNHYKK 309
ELE LQ+ ++++ ++K ++E +K
Sbjct: 91 ELEAKIAELQRIEEELRDKLKHLIEALCGFKL 122
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 28.1 bits (64), Expect = 7.0
Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 247 DQIAKLKAKRRTLKNRGYA----QNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVE 302
D++ +L +RR L+ +N SK + Q + + L +++++K EIK +
Sbjct: 28 DELLELDEERRELQTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKELKEEIKALEA 87
Query: 303 ERNHYKKQYE 312
E + + + E
Sbjct: 88 ELDELEAELE 97
>gnl|CDD|153289 cd07605, I-BAR_IMD, Inverse (I)-BAR, also known as the IRSp53/MIM
homology Domain (IMD), a dimerization module that binds
and bends membranes. Inverse (I)-BAR (or IMD) is a
member of the Bin/Amphiphysin/Rvs (BAR) domain family.
It is a dimerization and lipid-binding module that bends
membranes and induces membrane protrusions in the
opposite direction compared to classical BAR and F-BAR
domains, which produce membrane invaginations. IMD
domains are found in Insulin Receptor tyrosine kinase
Substrate p53 (IRSp53), Missing in Metastasis (MIM), and
Brain-specific Angiogenesis Inhibitor 1-Associated
Protein 2-like (BAIAP2L) proteins. These are
multi-domain proteins that act as scaffolding proteins
and transducers of a variety of signaling pathways that
link membrane dynamics and the underlying actin
cytoskeleton. Most members contain an N-terminal IMD, an
SH3 domain, and a WASP homology 2 (WH2) actin-binding
motif at the C-terminus, exccept for MIM which does not
carry an SH3 domain. Some members contain additional
domains and motifs. The IMD domain binds and bundles
actin filaments, binds membranes and produces membrane
protrusions, and interacts with the small GTPase Rac.
Length = 223
Score = 27.7 bits (62), Expect = 7.3
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 275 QRQELEVTNKHLQQQLQK-MKSEIKQIVEERNHYKKQYEIVMRNKDRSEAE 324
Q + + L L+K ++ + K I + YKK+Y+ + D++ +E
Sbjct: 84 LEQVAKAFHGELILPLEKKLELDQKVINKFEKDYKKEYKQKREDLDKARSE 134
>gnl|CDD|152554 pfam12119, DUF3581, Protein of unknown function (DUF3581). This
protein is found in bacteria. Proteins in this family
are about 240 amino acids in length.
Length = 218
Score = 27.6 bits (62), Expect = 7.5
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 166 EEVPLDMRRHCAADWSLVDEHGGKYLH 192
++VPL +S+ DE G YL
Sbjct: 74 DDVPLIFPEAVDESFSITDEKGKVYLE 100
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 28.0 bits (63), Expect = 7.6
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 271 KRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYEIVMRNKDRSEAE 324
KR Q+QEL+ + +Q +K + ++ EE ++ E + E E
Sbjct: 227 KRRRQKQELQRARE--EQIEEKEERLQEERAEEEAERERMLE-KQAEDEELEQE 277
>gnl|CDD|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed.
Length = 356
Score = 27.8 bits (61), Expect = 7.6
Identities = 13/33 (39%), Positives = 16/33 (48%)
Query: 111 TPGTPPDTPPGSNSPPHQHYHHMDHPSHPHIQQ 143
TP T TPP +N+P D P P I+Q
Sbjct: 127 TPKTKVTTPPSTNTPQPMQSTKSDTPQSPTIKQ 159
>gnl|CDD|220410 pfam09798, LCD1, DNA damage checkpoint protein. This is a family
of proteins which regulate checkpoint kinases. In
Schizosaccharomyces pombe this protein is called Rad26
and in Saccharomyces cerevisiae it is called LCD1.
Length = 648
Score = 28.2 bits (63), Expect = 7.8
Identities = 20/85 (23%), Positives = 42/85 (49%), Gaps = 10/85 (11%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEER- 304
RD++ L+ +++ +N+ Q R L ++ + E+ + L+Q+LQ ++ E K +V E+
Sbjct: 3 RDKLDMLQQQKQEERNK---QKSRVNELKEKHDQEL--QKLKQELQSLEDERKFLVLEQR 57
Query: 305 ----NHYKKQYEIVMRNKDRSEAEH 325
N + + S+A H
Sbjct: 58 GLSANDLRTELSPPSNLLKTSDASH 82
>gnl|CDD|214699 smart00503, SynN, Syntaxin N-terminal domain. Three-helix domain
that (in Sso1p) slows the rate of its reaction with the
SNAP-25 homologue Sec9p.
Length = 117
Score = 26.9 bits (60), Expect = 7.9
Identities = 10/78 (12%), Positives = 30/78 (38%), Gaps = 9/78 (11%)
Query: 246 RDQIAKLKAKRRTLKNRGYAQNCRSKRLH-----QRQELEVTNKHLQQQLQKMKSEIKQI 300
R I K+ L+ + R++LE +++ +++++++K++
Sbjct: 14 RANIQKISQNVAELQK----LHEELLTPPDADKELREKLERLIDDIKRLAKEIRAKLKEL 69
Query: 301 VEERNHYKKQYEIVMRNK 318
+E + R +
Sbjct: 70 EKENLENRASGSASDRTR 87
>gnl|CDD|220180 pfam09325, Vps5, Vps5 C terminal like. Vps5 is a sorting nexin
that functions in membrane trafficking. This is the C
terminal dimerisation domain.
Length = 236
Score = 27.6 bits (62), Expect = 7.9
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 264 YAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYKKQYE 312
A+ SK+ Q +L+ K Q +LQ+ K E+ + + KK++E
Sbjct: 139 NAEQDLSKKRAQLAKLKGAGKSRQDKLQQAKKEVDEAERKVQQAKKEFE 187
>gnl|CDD|222449 pfam13908, Shisa, Wnt and FGF inhibitory regulator. Shisa is a
transcription factor-type molecule that physically
interacts with immature forms of the Wnt receptor
Frizzled and the FGF receptor within the endoplasmic
reticulum to inhibit their post-translational maturation
and trafficking to the cell surface.
Length = 177
Score = 27.5 bits (61), Expect = 8.0
Identities = 15/53 (28%), Positives = 19/53 (35%), Gaps = 3/53 (5%)
Query: 112 PGTPPDTPPGSNSPPHQHYHHMDHPSHPHIQQLP-PRAQTYHDMFMPPHPNPF 163
PP T P P +Q YH M P P + P + P P P+
Sbjct: 127 LPQPPSTAPSYPGPQYQGYHPM--PPQPGMPAPPYSLQYPPPGLLQPQGPPPY 177
>gnl|CDD|235122 PRK03378, ppnK, inorganic polyphosphate/ATP-NAD kinase;
Provisional.
Length = 292
Score = 27.6 bits (62), Expect = 8.4
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 5/32 (15%)
Query: 65 SIPVPNGGSVHIQSPPHHLLTPPGSSIHPQDY 96
++P+ G V I+ +HL + IHP+DY
Sbjct: 249 ALPIQPGEEVLIRRSDYHL-----NLIHPKDY 275
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 27.9 bits (62), Expect = 9.6
Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 10/78 (12%)
Query: 249 IAKLKAKRRTLKNRGYAQNCRSKRLHQRQELEVTNKHLQQQLQKMKSEIKQIVEERNHYK 308
I KL A + L+ + ++ +E E K L+Q+++++K + E K
Sbjct: 517 IEKLSALEKELEQK--NEHLEKLL----KEQEKLKKELEQEMEELKERERNKKLEL--EK 568
Query: 309 KQYEIVMRNKDRSEAEHL 326
+ E + + E E +
Sbjct: 569 EAQEAL--KALKKEVESI 584
>gnl|CDD|131493 TIGR02440, FadJ, fatty oxidation complex, alpha subunit FadJ.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Plays a minor role in aerobic beta-oxidation of fatty
acids. FadJI complex is necessary for anaerobic growth
on short-chain acids with nitrate as an electron
acceptor. Activities include: enoyl-CoA hydratase (EC
4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadJ (aka YfcX). This model
excludes the FadB of TIGR02437 equivalog model [Fatty
acid and phospholipid metabolism, Degradation].
Length = 699
Score = 27.9 bits (62), Expect = 9.6
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 32 FEDVNVKREIINNNEQDATNHNI--SNHQRLP 61
FED+ +K +++ + EQ+ H I SN LP
Sbjct: 393 FEDLALKHQMVKDIEQECAAHTIFASNTSSLP 424
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
0.315 0.131 0.398
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,007,247
Number of extensions: 1629242
Number of successful extensions: 3137
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2974
Number of HSP's successfully gapped: 260
Length of query: 328
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 231
Effective length of database: 6,635,264
Effective search space: 1532745984
Effective search space used: 1532745984
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: 59 (26.4 bits)