RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4518
(376 letters)
>gnl|CDD|216454 pfam01363, FYVE, FYVE zinc finger. The FYVE zinc finger is named
after four proteins that it has been found in: Fab1,
YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been
shown to bind two Zn++ ions. The FYVE finger has eight
potential zinc coordinating cysteine positions. Many
members of this family also include two histidines in a
motif R+HHC+XCG, where + represents a charged residue
and X any residue. We have included members which do
not conserve these histidine residues but are clearly
related.
Length = 68
Score = 72.0 bits (177), Expect = 3e-16
Identities = 17/40 (42%), Positives = 23/40 (57%)
Query: 53 VPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCS 92
W+ DV C C + F+F +R+HHCR CG + C CS
Sbjct: 1 PRWVPDSDVTNCMGCGKPFSFFRRRHHCRNCGKVFCSSCS 40
>gnl|CDD|214499 smart00064, FYVE, Protein present in Fab1, YOTB, Vac1, and EEA1.
The FYVE zinc finger is named after four proteins where
it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1.
The FYVE finger has been shown to bind two Zn2+ ions.
The FYVE finger has eight potential zinc coordinating
cysteine positions. The FYVE finger is structurally
related to the PHD finger and the RING finger. Many
members of this family also include two histidines in a
motif R+HHC+XCG, where + represents a charged residue
and X any residue. The FYVE finger functions in the
membrane recruitment of cytosolic proteins by binding to
phosphatidylinositol 3-phosphate (PI3P), which is
prominent on endosomes. The R+HHC+XCG motif is critical
for PI3P binding.
Length = 68
Score = 65.1 bits (159), Expect = 1e-13
Identities = 21/50 (42%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 54 PWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCS-FFLPLNKARQ 102
W+ ++V C C + FN KR+HHCR CG I C CS PL K
Sbjct: 3 HWIPDEEVSNCMGCGKEFNLTKRRHHCRNCGRIFCSKCSSKKAPLPKLGI 52
>gnl|CDD|238022 cd00065, FYVE, FYVE domain; Zinc-binding domain; targets proteins
to membrane lipids via interaction with
phosphatidylinositol-3-phosphate, PI3P; present in
Fab1, YOTB, Vac1, and EEA1;.
Length = 57
Score = 60.9 bits (148), Expect = 3e-12
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 60 DVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCS 92
D C C + F +R+HHCR CG I C CS
Sbjct: 1 DASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCS 33
>gnl|CDD|151903 pfam11464, Rbsn, Rabenosyn Rab binding domain. Rabenosyn-5 (Rbsn)
is a multivalent effector with interacts with the Rab
family.Rsbn contains distinct Rab4 and Rab5 binding
sites within residues 264-500 and 627-784 respectively.
Rab proteins are GTPases involved in the regulation of
all stages of membrane trafficking.
Length = 42
Score = 48.6 bits (116), Expect = 5e-08
Identities = 22/42 (52%), Positives = 34/42 (80%)
Query: 322 LVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQ 363
L+QQI NIK +I++AR A R++EV +LE +L+ELQ+E + +Q
Sbjct: 1 LLQQINNIKGYIRQARQAGRFDEVETLEENLRELQDELYEQQ 42
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 35.1 bits (80), Expect = 0.064
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 57 DGKDVPRCPNCSRSF-----NFAKRQHHCRLCGCIMCHDC 91
D + CP+C R+F R HHCR CG +C C
Sbjct: 456 DDESSDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFC 495
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 34.4 bits (80), Expect = 0.10
Identities = 25/120 (20%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 254 RLAELREE-RRLAEEARQREEAIRE---LRGREENFNVETHHGRHSVSKENNVSLLEAWS 309
++ E EE +R+ EEA++ EAI++ L +EE + + + N + LE
Sbjct: 32 KIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLE--- 88
Query: 310 PAGTKSVSSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQEQQTE 369
+ + ++ L +++ +++ +E + + E+ + L++ +EE +EQ E
Sbjct: 89 ---KRLLQKEENLDRKLELLEK--REEELEKKEKELEQKQQELEKKEEELEELIEEQLQE 143
>gnl|CDD|223572 COG0498, ThrC, Threonine synthase [Amino acid transport and
metabolism].
Length = 411
Score = 33.8 bits (78), Expect = 0.12
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 63 RCPNCSRSFNFAKRQHHCRLCG 84
RC C R F+ A Q C CG
Sbjct: 7 RCLKCGREFSQALLQGLCPDCG 28
>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated.
Length = 740
Score = 33.6 bits (77), Expect = 0.17
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 46 KNHEQAIVPWLDG----KDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKAR 101
KN E+ +G K + +CP C + + R GC +C+F LPL K+
Sbjct: 570 KNREKIRESLREGLREDKIIGKCPLCGSDLMVRRSKRGSRFIGCEGYPECTFSLPLPKSG 629
Query: 102 QILV 105
QI+V
Sbjct: 630 QIIV 633
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 505
Score = 32.7 bits (75), Expect = 0.33
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 6/36 (16%)
Query: 61 VPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLP 96
+ CPNC S + K++ + CH C + P
Sbjct: 222 ILCCPNCDVSLTYHKKEGK------LRCHYCGYQEP 251
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 31.9 bits (73), Expect = 0.55
Identities = 38/191 (19%), Positives = 69/191 (36%), Gaps = 20/191 (10%)
Query: 99 KARQILVE--PELGESQLSASANSDLNLRLLESREVLKESRNSRPLICDLYDALMGKKQE 156
KA Q+LVE E+ + + L L +R L+ +S+ I
Sbjct: 66 KAGQVLVELDATDVEADAAELESQVLRLEAEVAR--LRAEADSQAAIEF----------- 112
Query: 157 ASKLRAMYLEMIDSLLAGETMYYASDAQALRVKLVRLAENIDTISNKVTTLSSASGAQQA 216
L + + L+ G+ + S LR +L + I + ++ L + QA
Sbjct: 113 PDDLLSAEDPAVPELIKGQQSLFESRKSTLRAQLELILAQIKQLEAELAGLQA---QLQA 169
Query: 217 SDSPMTMSQRLHKSIRQ-ASTNFI-RTHLLTLPNVPSDERLAELREERRLAEEARQREEA 274
+ + ++ R+ + R LL L ++ + R E L RQ +E
Sbjct: 170 LRQQLEVISEELEARRKLKEKGLVSRLELLELERERAEAQGELGRLEAELEVLKRQIDEL 229
Query: 275 IRELRGREENF 285
E + E+ F
Sbjct: 230 QLERQQIEQTF 240
>gnl|CDD|227598 COG5273, COG5273, Uncharacterized protein containing DHHC-type Zn
finger [General function prediction only].
Length = 309
Score = 31.6 bits (72), Expect = 0.67
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 11/46 (23%)
Query: 56 LDGKDVPR--CPNCSRSFNFAK--RQHHCRLCG-CIMCHD--CSFF 94
DGK C C N K R HHC +C C++ D C +
Sbjct: 102 DDGKFGTENFCSTC----NIYKPPRSHHCSICNRCVLKFDHHCPWI 143
>gnl|CDD|216039 pfam00643, zf-B_box, B-box zinc finger.
Length = 42
Score = 28.2 bits (63), Expect = 0.83
Identities = 6/33 (18%), Positives = 11/33 (33%), Gaps = 4/33 (12%)
Query: 59 KDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDC 91
CP + +C C ++C +C
Sbjct: 1 SKERLCPEHEE----KPLELYCEDCQQLLCEEC 29
>gnl|CDD|197698 smart00396, ZnF_UBR1, Putative zinc finger in N-recognin, a
recognition component of the N-end rule pathway.
Domain is involved in recognition of N-end rule
substrates in yeast Ubr1p.
Length = 71
Score = 28.6 bits (64), Expect = 1.2
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 4/31 (12%)
Query: 66 NCSRSFNFAKRQHHCRLCG----CIMCHDCS 92
C F + + C+ CG C++C DC
Sbjct: 2 VCGYKFTGGEVIYRCKTCGLDPTCVLCSDCF 32
>gnl|CDD|224526 COG1610, COG1610, Uncharacterized conserved protein [Function
unknown].
Length = 148
Score = 29.6 bits (67), Expect = 1.3
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 12/75 (16%)
Query: 221 MTMSQRLHKSIRQA-------STNFIRTHLLTLPNVPSDERLAELREERR---LAEEARQ 270
M++ ++L + +++A IR L + DER EL +E LA+E +Q
Sbjct: 1 MSLKEKLTEDLKEAMKAKDKDRLGTIRLILAAIKQEEIDERKDELDDEEILKVLAKEIKQ 60
Query: 271 REEAIRELR--GREE 283
R ++ E GR++
Sbjct: 61 RRDSAEEYEKAGRQD 75
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 30.1 bits (68), Expect = 2.3
Identities = 23/116 (19%), Positives = 50/116 (43%), Gaps = 16/116 (13%)
Query: 252 DERLAELREERRLAEEARQREEAIRELRGREENFNVETHHGRHSVSKENNVSLLEAWSPA 311
+++L +L + AE ++ + +REL ++ +E +S LE
Sbjct: 199 EKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEE-ELSRLEE---- 253
Query: 312 GTKSVSSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQEQQ 367
+ L +++ ++ I+E + +E+ L L+ELQEE ++E +
Sbjct: 254 ------ELEELQEELEEAEKEIEELK-----SELEELREELEELQEELLELKEEIE 298
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 30.0 bits (68), Expect = 2.7
Identities = 8/26 (30%), Positives = 9/26 (34%), Gaps = 2/26 (7%)
Query: 61 VPRCPNCSRSFNFAKRQHH--CRLCG 84
+ CPNC K C CG
Sbjct: 444 IAECPNCDSPLTLHKATGQLRCHYCG 469
>gnl|CDD|226559 COG4073, COG4073, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 198
Score = 29.0 bits (65), Expect = 2.8
Identities = 17/38 (44%), Positives = 20/38 (52%)
Query: 244 LTLPNVPSDERLAELREERRLAEEARQREEAIRELRGR 281
L +P SD L + E L E+R REE I ELR R
Sbjct: 142 LEIPRRGSDRSLDVVSEILGLIAESRTREEFIEELRRR 179
>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 = 29.6 bits (67), Expect = 3.0
Identities = 30/115 (26%), Positives = 49/115 (42%), Gaps = 7/115 (6%)
Query: 252 DERLAELREERRLAEEARQREEAIRELRGREENFNVETHHGRHSVSKENN-VSLLEAWSP 310
+ AEL E EE R E + E E + ++ NN + LEA
Sbjct: 354 ESLEAELEELEAELEELESRLEELEEQL---ETLRSKVAQLELQIASLNNEIERLEA--- 407
Query: 311 AGTKSVSSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQE 365
+ ++ L Q+I + + ++EA + E+ LE L+ELQEE R ++
Sbjct: 408 RLERLEDRRERLQQEIEELLKKLEEAELKELQAELEELEEELEELQEELERLEEA 462
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 29.5 bits (67), Expect = 3.0
Identities = 17/45 (37%), Positives = 20/45 (44%), Gaps = 11/45 (24%)
Query: 250 PSDERLAELREERRLAEEA---------RQRE--EAIRELRGREE 283
DERLAELR E E +++E EAI LR E
Sbjct: 447 DHDERLAELRAELAALEAELAALEARWQQEKELVEAILALRAELE 491
>gnl|CDD|227204 COG4867, COG4867, Uncharacterized protein with a von Willebrand
factor type A (vWA) domain [General function prediction
only].
Length = 652
Score = 29.6 bits (66), Expect = 3.2
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 238 FIRTHLLTLPNVPSDERLAELREERRLAEEARQREEAIRELRGRE 282
F L LP P+ + + EL E R + +AR++ E I++L GRE
Sbjct: 116 FAELQLDALPESPA-KAVQELAEYRWRSGQAREKYEQIKDLLGRE 159
>gnl|CDD|211920 TIGR04197, T7SS_SACOL2603, type VII secretion effector, SACOL2603
family. Members of this protein family are similar in
length and sequence (although remotely) to the WXG100
family of type VII secretion system (T7SS) targets,
described by family TIGR03930. Phylogenetic profiling
shows that members of this family are similarly
restricted to species with T7SS, marking this family as
a related set of T7SS effectors. Members include
SACOL2603 from Staphylococcus aureus subsp. aureus COL.
Oddly, members of family pfam10824 (DUF2580), which
appears also to be related, seem not to be tied to T7SS.
Length = 85
Score = 27.2 bits (61), Expect = 3.5
Identities = 13/59 (22%), Positives = 26/59 (44%)
Query: 179 YASDAQALRVKLVRLAENIDTISNKVTTLSSASGAQQASDSPMTMSQRLHKSIRQASTN 237
A A++ L+ + TTL+ + A +A D T+ ++ ++ Q +TN
Sbjct: 8 AQQHATAIKSASSALSGVGSVTKDDQTTLTGNTNAHEAIDQLQTLVSQIQSALEQDATN 66
>gnl|CDD|223059 PHA03367, PHA03367, single-stranded DNA binding protein;
Provisional.
Length = 1115
Score = 29.6 bits (67), Expect = 3.7
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 146 LYDALMGKKQEASKLRAMYLEMIDSLLAGETMYYA---SDAQALRVKLVR 192
LYD + +K +LR Y + E ++Y+ S AQALRV+ V+
Sbjct: 184 LYDETLFEKTSFVQLRGFYNPAVS-----EYLFYSLYTSWAQALRVRDVK 228
>gnl|CDD|219628 pfam07898, DUF1676, Protein of unknown function (DUF1676). This
family contains sequences derived from proteins of
unknown function expressed by Drosophila melanogaster
and Anopheles gambiae.
Length = 112
Score = 27.8 bits (62), Expect = 4.2
Identities = 14/98 (14%), Positives = 32/98 (32%), Gaps = 3/98 (3%)
Query: 185 ALRVKLVRLAENIDTISNKVTTLSS--ASGAQQASDSPMTMSQRLHKSIRQASTNFIRTH 242
L + L + + + N S A + + ++ + L K + F+R+H
Sbjct: 9 VLDSDSISLTDGVSLVRNPEAPQRSTEAESRSLSEEDSVSREEELDKLLLDRLERFLRSH 68
Query: 243 LLTLPNVPSDERLAELREERRLAEEARQREEAIRELRG 280
L + +P R + ++L+
Sbjct: 69 SLQV-KLPEATGSGAASARRPDLRALEEGRGKKKKLKK 105
>gnl|CDD|192718 pfam11176, DUF2962, Protein of unknown function (DUF2962). This
eukaryotic family of proteins has no known function.
Length = 155
Score = 28.4 bits (64), Expect = 4.2
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 5/60 (8%)
Query: 251 SDERLAELREERRLAEEARQREEAIRELRGREENFNVETHHGRH--SVSKENNVSLLEAW 308
DE L +L+ ERR RE+ + + +E E G ++ +NV L W
Sbjct: 82 FDEELEQLKSERRPGRPPSSREDVLEQTIEKERK---EFETGFEIPDLTDADNVKALREW 138
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 29.2 bits (66), Expect = 4.4
Identities = 13/74 (17%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 310 PAGTKSVSSQDPLVQQITNIKQ--FIKEARMAHRYNEVASLENHLKELQ------EEYFR 361
P G D Q ++ ++ R+ + + L++L+ E+F+
Sbjct: 539 PDGPSVWKLDDKEELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAKIPPAEFFK 598
Query: 362 RQQEQQTEVNDSGL 375
RQ+++ + +++GL
Sbjct: 599 RQEDKYSAFDETGL 612
>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein. Members of
this family are long (~850 residue) bacterial proteins
from the alpha Proteobacteria. Each has 2-3 predicted
transmembrane helices near the N-terminus and a long
C-terminal region that includes stretches of
Gln/Gly-rich low complexity sequence, predicted by TMHMM
to be outside the membrane. In Bradyrhizobium japonicum,
two tandem reading frames are together homologous the
single members found in other species; the cutoffs
scores are set low enough that the longer scores above
the trusted cutoff and the shorter above the noise
cutoff for this model.
Length = 851
Score = 29.2 bits (65), Expect = 4.5
Identities = 47/255 (18%), Positives = 95/255 (37%), Gaps = 36/255 (14%)
Query: 126 LLESREVLKESRNSRPLICDLYDALMGKKQEASKLRAMYLEMIDSLLAGETMYYASDAQA 185
+ E R +L N + D DAL+ +E YL +
Sbjct: 422 VAEQRRILALDANQNSQVYDALDALLLAPEETIPNAGHYLGL----------------YT 465
Query: 186 LRVKLVRLAENIDTISNKVTTLSSASGAQQASDSPMTMSQRLHKSIRQASTNFIRTHLLT 245
+R +L A D + + L S A D ++ ++R ++ + A +
Sbjct: 466 IRTRL-ERARTDDALRDVADNLWSL--ALGIEDGDLSDAERRLRAAQDALKD-------A 515
Query: 246 LPNVPSDERLAELREERRLAEEARQREEAIRELRGREENFNVETHHGRHSVSK--ENNVS 303
L SDE + +L ++ R A + R+ A + ++ + + + +N +
Sbjct: 516 LERGASDEEIKQLTDKLRAAMQTYMRQLAQQLRNNPQQLARPLDPNTKVLRQQDLQNMMD 575
Query: 304 LLEAWSPAGTKSVSSQ--DPLVQQITNIK--QFIKEARMAHRYNEVASLENHLKELQEEY 359
+E + +G + + Q L Q + N++ Q + +M + ++ N L EL
Sbjct: 576 QIENLARSGDRDQAKQLLSQLQQMMNNLQMGQPGQGQQMGDQSGDMEQQMNKLGEL---- 631
Query: 360 FRRQQEQQTEVNDSG 374
R+QQ+ + E
Sbjct: 632 MRKQQQLRDETFKLD 646
>gnl|CDD|206084 pfam13913, zf-C2HC_2, zinc-finger of a C2HC-type. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 25
Score = 25.6 bits (57), Expect = 4.6
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 63 RCPNCSRSFNFAKRQHHCRLC 83
CP C R F + H ++C
Sbjct: 4 PCPICGRKFAPDRLAKHEKVC 24
>gnl|CDD|216554 pfam01529, zf-DHHC, DHHC palmitoyltransferase. This family
includes the well known DHHC zinc binding domain as
well as three of the four conserved transmembrane
regions found in this family of palmitoyltransferase
enzymes.
Length = 167
Score = 28.2 bits (63), Expect = 4.8
Identities = 17/70 (24%), Positives = 25/70 (35%), Gaps = 19/70 (27%)
Query: 40 IDP--IKKKNHEQAIVP------WLDGKDVPR--CPNCSRSFNFAK--RQHHCRLCG-CI 86
DP + K E+ ++ C C N K R HHCR+C C+
Sbjct: 10 TDPGYVPKNPTEKEQEKQPDEESEEGDEEDELKFCSTC----NIIKPPRSHHCRVCNRCV 65
Query: 87 MCHD--CSFF 94
+ D C +
Sbjct: 66 LRFDHHCPWL 75
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1042
Score = 28.8 bits (64), Expect = 5.7
Identities = 23/117 (19%), Positives = 49/117 (41%), Gaps = 9/117 (7%)
Query: 253 ERLAELREERRLAEEARQREEAIRELRGREENFNVETHHGRHSVSKENNVSLLEAWSP-- 310
+ A L ++R EE ++++ +++LR R E ++E ++ +P
Sbjct: 240 QSHAYLTQKREAQEEQLKKQQLLKQLRARIEEL--RAQEAVLEETQE-RINRARKAAPLA 296
Query: 311 AGTKSVSSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQEQQ 367
A K+V+ + QQ I ++ +M R + H+K+ +R+ Q
Sbjct: 297 AHIKAVTQIE---QQAQRIHTELQS-KMRSRAKLLMKRAAHVKQQSSIEEQRRLLQT 349
>gnl|CDD|221513 pfam12296, HsbA, Hydrophobic surface binding protein A. This
protein is found in eukaryotes. Proteins in this family
are typically between 171 to 275 amino acids in length.
Although the HsbA amino acid sequence suggests that HsbA
may be hydrophilic, HsbA adsorbed to hydrophobic PBSA
(Polybutylene succinate-co-adipate) surfaces in the
presence of NaCl or CaCl2. When HsbA was adsorbed on the
hydrophobic PBSA surfaces, it promoted PBSA degradation
via the CutL1 polyesterase. CutL1 interacts directly
with HsbA attached to the hydrophobic QCM electrode
surface. These results suggest that when HsbA is
adsorbed onto the PBSA surface, it recruits CutL1, and
that when CutL1 is accumulated on the PBSA surface, it
stimulates PBSA degradation.
Length = 124
Score = 27.2 bits (61), Expect = 6.1
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 197 IDTISNKVTTLSSASGAQQASDSPMTM----SQRLHKSIRQASTN 237
I+ IS+ VT L ++ A D S L +I+QA+T+
Sbjct: 10 INNISDAVTALDTSINAYTGGDLGALPILSASTTLISAIKQATTD 54
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 28.8 bits (65), Expect = 6.2
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 255 LAELREERRLAEEARQREEAIRELRGREE 283
+ + +E++ AEEA+ R EA R+ R E
Sbjct: 438 IRAIEQEKKKAEEAKARFEA-RQARLERE 465
>gnl|CDD|181205 PRK08040, PRK08040, putative semialdehyde dehydrogenase;
Provisional.
Length = 336
Score = 28.5 bits (64), Expect = 6.8
Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 18/76 (23%)
Query: 204 VTTLSSASG-AQQASDSPMTMSQRLHKSI--------RQASTNFIRTHLLTLPNVPSDER 254
VT L SAS + A D+ S +L I RQ + N LP +P E
Sbjct: 155 VTNLLSASAHGKAAVDALAGQSAKLLNGIPIEEGFFGRQLAFNM-------LPLLPDSE- 206
Query: 255 LAELREERRLAEEARQ 270
+REERRL ++ R+
Sbjct: 207 -GSVREERRLVDQVRK 221
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 28.5 bits (65), Expect = 7.4
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 253 ERLAELREERRLAEEARQREEAIRELRGREENFNV 287
E L EL E LA+ + E+ I EL G E FN+
Sbjct: 503 EYLKELSAE--LAQRLAELEQEIYELAGEE--FNI 533
>gnl|CDD|227781 COG5494, COG5494, Predicted thioredoxin/glutaredoxin
[Posttranslational modification, protein turnover,
chaperones].
Length = 265
Score = 27.9 bits (62), Expect = 7.6
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 342 YNEVASLENHLKELQEEYFRRQQEQQTEV 370
V N L E +E F R Q++Q E+
Sbjct: 226 VMRVLEAYNFLLENGDEIFNRVQKEQMEI 254
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 28.3 bits (63), Expect = 8.5
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 242 HLLTLPNVPSDERLAELREE--RRLAEEARQREEAIR 276
H + N+P + E + R+L EE R REEAIR
Sbjct: 415 HAIVPNNIPEELYWVEEEHQIYRKLQEERRLREEAIR 451
>gnl|CDD|217297 pfam02945, Endonuclease_7, Recombination endonuclease VII.
Length = 81
Score = 26.3 bits (58), Expect = 9.5
Identities = 11/47 (23%), Positives = 12/47 (25%), Gaps = 12/47 (25%)
Query: 50 QAIVPWLDGKDVPRCPNCSRSFNFAKRQH--HCRLCG------CIMC 88
AI G RC C R+ H G C C
Sbjct: 16 WAIYEAQGG----RCAICQRANGGTPALAVDHDHKTGHVRGLLCGPC 58
>gnl|CDD|188689 cd08735, RGS_AKAP2_1, Regulator of G protein signaling (RGS)
domain 1 found in the A-kinase anchoring protein,
D-AKAP2. The RGS (Regulator of G-protein Signaling)
domain is an essential part of the D-AKAP2 (A-kinase
anchoring protein), a member of the RGS protein family.
They are a diverse group of multifunctional proteins
that regulate cellular signaling events downstream of
G-protein coupled receptors (GPCRs). RGS proteins
regulate many aspects of embryonic development such as
glial differentiation, embryonic axis formation,
skeletal and muscle development, cell migration during
early embryogenesis, as well as apoptosis, cell
proliferation, and modulation of cardiac development.
D-AKAP2 contains two RGS domains which play an
important role in spatiotemporal localization of
cAMP-dependent PKA (cyclic AMP-dependent protein
kinase) that regulates many different signaling
pathways by phosphorylation of target proteins. This cd
contains the first RGS domain.
Length = 171
Score = 27.4 bits (61), Expect = 9.7
Identities = 8/41 (19%), Positives = 15/41 (36%)
Query: 39 PIDPIKKKNHEQAIVPWLDGKDVPRCPNCSRSFNFAKRQHH 79
++ +K + E+ + P LD K + S S
Sbjct: 52 SLNTVKHSSLEEPVSPSLDRKVLESKSTDSLSQRLTDDDDE 92
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.130 0.365
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,573,858
Number of extensions: 1770329
Number of successful extensions: 3327
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3233
Number of HSP's successfully gapped: 156
Length of query: 376
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 278
Effective length of database: 6,590,910
Effective search space: 1832272980
Effective search space used: 1832272980
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 (21.7 bits)
S2: 60 (26.9 bits)