RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16233
(464 letters)
>gnl|CDD|115363 pfam06701, MIB_HERC2, Mib_herc2. Named "mib/herc2 domain" in.
Usually the protein also contains an E3 ligase domain
(either Ring or Hect).
Length = 63
Score = 80.5 bits (199), Expect = 4e-19
Identities = 34/63 (53%), Positives = 45/63 (71%), Gaps = 3/63 (4%)
Query: 7 GLRVIRGPDWKWLDEDGGEGGLGTVVAVKS--NVVSVIWDLGNKSSCYRVGSENAYDLQV 64
G RV+RG DWKW D+DGGEGG GTV ++S V V WD G+ +S YR+G+E YDL++
Sbjct: 1 GARVVRGVDWKWGDQDGGEGGEGTVTEIESPDGWVVVQWDTGSTNS-YRMGAEGKYDLKL 59
Query: 65 YDS 67
D+
Sbjct: 60 ADN 62
Score = 71.2 bits (175), Expect = 1e-15
Identities = 28/66 (42%), Positives = 36/66 (54%), Gaps = 6/66 (9%)
Query: 150 GAKVSRGLNWEWENQDGGPGKTGRIISIEDGKVGKSYRSVAKVLWSIGKENIYRIGSYGK 209
GA+V RG++W+W +QDGG G G + IE S V W G N YR+G+ GK
Sbjct: 1 GARVVRGVDWKWGDQDGGEGGEGTVTEIE------SPDGWVVVQWDTGSTNSYRMGAEGK 54
Query: 210 VDLKCV 215
DLK
Sbjct: 55 YDLKLA 60
>gnl|CDD|239079 cd02339, ZZ_Mind_bomb, Zinc finger, ZZ type. Zinc finger present in
Drosophila Mind bomb (D-mib) and related proteins. The
ZZ motif coordinates two zinc ions and most likely
participates in ligand binding or molecular scaffolding.
Mind bomb is an E3 ubiqitin ligase that has been shown
to regulate signaling by the Notch ligand Delta in
Drosophila melanogaster.
Length = 45
Score = 69.8 bits (171), Expect = 2e-15
Identities = 26/46 (56%), Positives = 33/46 (71%), Gaps = 2/46 (4%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFYR 122
I CD C+ + I+G R+ C EC NYDLC +CYHGD+HD+ H FYR
Sbjct: 1 IICDTCR--KQGIIGIRWKCAECPNYDLCTTCYHGDKHDLEHRFYR 44
>gnl|CDD|239080 cd02340, ZZ_NBR1_like, Zinc finger, ZZ type. Zinc finger present in
Drosophila ref(2)P, NBR1, Human sequestosome 1 and
related proteins. The ZZ motif coordinates two zinc ions
and most likely participates in ligand binding or
molecular scaffolding. Drosophila ref(2)P appears to
control the multiplication of sigma rhabdovirus. NBR1
(Next to BRCA1 gene 1 protein) interacts with
fasciculation and elongation protein zeta-1 (FEZ1) and
calcium and integrin binding protein (CIB), and may
function in cell signalling pathways. Sequestosome 1 is
a phosphotyrosine independent ligand for the Lck SH2
domain and binds noncovalently to ubiquitin via its UBA
domain.
Length = 43
Score = 58.8 bits (143), Expect = 1e-11
Identities = 20/47 (42%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFYRV 123
+ CD CQ IVG RY C+ C +YDLC SC H HA ++
Sbjct: 1 VICDGCQ---GPIVGVRYKCLVCPDYDLCESCEAKGVHP-EHAMLKI 43
>gnl|CDD|239078 cd02338, ZZ_PCMF_like, Zinc finger, ZZ type. Zinc finger present in
potassium channel modulatory factor (PCMF) 1 and
related proteins. The ZZ motif coordinates two zinc ions
and most likely participates in ligand binding or
molecular scaffolding. Human potassium channel
modulatory factor 1 or FIGC has been shown to possess
intrinsic E3 ubiquitin ligase activity and to promote
ubiquitination.
Length = 49
Score = 55.8 bits (135), Expect = 2e-10
Identities = 19/48 (39%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGD----EHDITHAF 120
+SCD C +S G RY C+ C +YDLCA CY H H
Sbjct: 1 VSCDGCG--KSNFTGRRYKCLICYDYDLCADCYDSGVTTERHLFDHPM 46
>gnl|CDD|239069 cd02249, ZZ, Zinc finger, ZZ type. Zinc finger present in
dystrophin, CBP/p300 and many other proteins. The ZZ
motif coordinates one or two zinc ions and most likely
participates in ligand binding or molecular scaffolding.
Many proteins containing ZZ motifs have other
zinc-binding motifs as well, and the majority serve as
scaffolds in pathways involving acetyltransferase,
protein kinase, or ubiqitin-related activity. ZZ
proteins can be grouped into the following functional
classes: chromatin modifying, cytoskeletal scaffolding,
ubiquitin binding or conjugating, and membrane receptor
or ion-channel modifying proteins.
Length = 46
Score = 55.5 bits (134), Expect = 2e-10
Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDE--HDITHAF 120
SCD C IVG RY C+ C ++DLC+SCY + H H+F
Sbjct: 1 YSCDGCLKP---IVGVRYHCLVCEDFDLCSSCYAKGKKGHPPDHSF 43
>gnl|CDD|197633 smart00291, ZnF_ZZ, Zinc-binding domain, present in Dystrophin,
CREB-binding protein. Putative zinc-binding domain
present in dystrophin-like proteins, and CREB-binding
protein/p300 homologues. The ZZ in dystrophin appears to
bind calmodulin. A missense mutation of one of the
conserved cysteines in dystrophin results in a patient
with Duchenne muscular dystrophy.
Length = 44
Score = 54.4 bits (131), Expect = 4e-10
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 73 KHETISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHA 119
H + SCD C IVG RY C+ C +YDLC SC+ H+
Sbjct: 1 VHHSYSCDTCG---KPIVGVRYHCLVCPDYDLCQSCFAKGSAGGEHS 44
>gnl|CDD|144236 pfam00569, ZZ, Zinc finger, ZZ type. Zinc finger present in
dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin.
Putative zinc finger; binding not yet shown. Four to six
cysteine residues in its sequence are responsible for
coordinating zinc ions, to reinforce the structure.
Length = 46
Score = 50.6 bits (121), Expect = 1e-08
Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 73 KHETISCDACQDERSCIVGTRYSCIECSNYDLCASCY 109
H +C+ C++ I+G RY C+ C +YDLC SC+
Sbjct: 1 IHHVYTCNICKEC--PIIGFRYHCLRCFDYDLCQSCF 35
>gnl|CDD|239084 cd02344, ZZ_HERC2, Zinc finger, ZZ type. Zinc finger present in
HERC2 and related proteins. HERC2 is a potential E3
ubiquitin protein ligase and/or guanine nucleotide
exchange factor. The ZZ motif coordinates two zinc ions
and most likely participates in ligand binding or
molecular scaffolding.
Length = 45
Score = 46.8 bits (111), Expect = 2e-07
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFYRV 123
++CD CQ I G R+ C C ++D C +C+ +H+ H F R+
Sbjct: 1 VTCDGCQ--MFPINGPRFKCRNCDDFDFCENCFKTRKHNTRHTFGRI 45
>gnl|CDD|239074 cd02334, ZZ_dystrophin, Zinc finger, ZZ type. Zinc finger present
in dystrophin and dystrobrevin. The ZZ motif coordinates
two zinc ions and most likely participates in ligand
binding or molecular scaffolding. Dystrophin attaches
actin filaments to an integral membrane glycoprotein
complex in muscle cells. The ZZ domain in dystrophin has
been shown to be essential for binding to the membrane
protein beta-dystroglycan.
Length = 49
Score = 46.2 bits (110), Expect = 4e-07
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCY----HGDEHDITH 118
C+ C++ I G RY C++C NYDLC SC+ H +H
Sbjct: 1 AKCNICKEFP--ITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSH 44
>gnl|CDD|239081 cd02341, ZZ_ZZZ3, Zinc finger, ZZ type. Zinc finger present in ZZZ3
(ZZ finger containing 3) and related proteins. The ZZ
motif coordinates two zinc ions and most likely
participates in ligand binding or molecular scaffolding.
Length = 48
Score = 42.0 bits (99), Expect = 1e-05
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSN--YDLCASCYH-GDEHDITH 118
CD+C I GTRY C EC + +DLC C G+ H H
Sbjct: 1 FKCDSC--GIEPIPGTRYHCSECDDGDFDLCQDCVVKGESHQEDH 43
>gnl|CDD|239083 cd02343, ZZ_EF, Zinc finger, ZZ type. Zinc finger present in
proteins with an EF_hand motif. The ZZ motif coordinates
two zinc ions and most likely participates in ligand
binding or molecular scaffolding.
Length = 48
Score = 40.4 bits (94), Expect = 5e-05
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 11/50 (22%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCY--------HGDEHDITH 118
ISCD C + RY C++C++ DLC +C+ H D+H++ +
Sbjct: 1 ISCDGCDEIAPW---HRYRCLQCTDMDLCKTCFLGGVKPEGHEDDHEMVN 47
>gnl|CDD|239085 cd02345, ZZ_dah, Zinc finger, ZZ type. Zinc finger present in
Drosophila dah and related proteins. The ZZ motif
coordinates two zinc ions and most likely participates
in ligand binding or molecular scaffolding. Dah
(discontinuous actin hexagon) is a membrane associated
protein essential for cortical furrow formation in
Drosophila. .
Length = 49
Score = 38.3 bits (89), Expect = 3e-04
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCY----HGDEHDITHAFY 121
+SC AC+ + I G R+ C C +Y LC CY H+ H Y
Sbjct: 1 LSCSACRKQD--ISGIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMY 47
>gnl|CDD|239075 cd02335, ZZ_ADA2, Zinc finger, ZZ type. Zinc finger present in
ADA2, a putative transcriptional adaptor, and related
proteins. The ZZ motif coordinates two zinc ions and
most likely participates in ligand binding or molecular
scaffolding.
Length = 49
Score = 38.0 bits (89), Expect = 3e-04
Identities = 18/51 (35%), Positives = 22/51 (43%), Gaps = 7/51 (13%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCY-HGDE---HDITHAFYRV 123
CD C + R C EC ++DLC C+ G E H H YRV
Sbjct: 1 YHCDYCSKD--ITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHN-YRV 48
>gnl|CDD|239077 cd02337, ZZ_CBP, Zinc finger, ZZ type. Zinc finger present in
CBP/p300 and related proteins. The ZZ motif coordinates
two zinc ions and most likely participates in ligand
binding or molecular scaffolding. CREB-binding protein
(CBP) is a large multidomain protein that provides
binding sites for transcriptional coactivators, the role
of the ZZ domain in CBP/p300 is unclear.
Length = 41
Score = 37.2 bits (86), Expect = 6e-04
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 78 SCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHD 115
+C+ C V TR+ C C +YDLC +CY+ H
Sbjct: 2 TCNEC----KHHVETRWHCTVCEDYDLCITCYNTKNHP 35
>gnl|CDD|239082 cd02342, ZZ_UBA_plant, Zinc finger, ZZ type. Zinc finger present in
plant ubiquitin-associated (UBA) proteins. The ZZ motif
coordinates a zinc ion and most likely participates in
ligand binding or molecular scaffolding.
Length = 43
Score = 33.3 bits (76), Expect = 0.015
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYH--GDEHDIT 117
I CD C I G RY +YDLC C+ G+E + T
Sbjct: 1 IQCDGCGVLP--ITGPRYKSKVKEDYDLCTICFSRMGNEGEYT 41
>gnl|CDD|237756 PRK14559, PRK14559, putative protein serine/threonine phosphatase;
Provisional.
Length = 645
Score = 37.0 bits (86), Expect = 0.025
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 372 TLSSKCLKLIKSNSLSDSTSLEITYRDYLLPFLNSQVN 409
+ L L+ S+ LSD+ LE ++ +LLP L+S N
Sbjct: 569 EIEEDTLLLLCSDGLSDNDLLETHWQTHLLPLLSSSAN 606
>gnl|CDD|227445 COG5114, COG5114, Histone acetyltransferase complex SAGA/ADA,
subunit ADA2 [Chromatin structure and dynamics].
Length = 432
Score = 33.9 bits (77), Expect = 0.16
Identities = 14/45 (31%), Positives = 17/45 (37%), Gaps = 2/45 (4%)
Query: 77 ISCDACQDERSCIVGTRYSCIECSNYDLCASCYHGDEHDITHAFY 121
I CD C + T C EC DLC C+ H+ Y
Sbjct: 6 IHCDVCFLD--MTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPY 48
>gnl|CDD|216175 pfam00888, Cullin, Cullin family.
Length = 603
Score = 31.4 bits (71), Expect = 1.2
Identities = 13/49 (26%), Positives = 17/49 (34%), Gaps = 9/49 (18%)
Query: 346 DLGDIGIVIKVYEDKDVRVAFRKNTWTLSSKCLKLIKSNSLSDSTSLEI 394
L I ++ K EDKDV F + L K S S +
Sbjct: 372 KLDKIIVLFKYIEDKDVFEKFYRK---------MLAKRLLNGTSASDDA 411
>gnl|CDD|239076 cd02336, ZZ_RSC8, Zinc finger, ZZ type. Zinc finger present in RSC8
and related proteins. RSC8 is a component of the RSC
complex, which is closely related to the SWI/SNF complex
and is involved in remodeling chromatin structure. The
ZZ motif coordinates a zinc ion and most likely
participates in ligand binding or molecular scaffolding.
Length = 45
Score = 27.7 bits (62), Expect = 1.4
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 92 TRYSCIECSNYDLCASCY 109
RY ++ YDLC SCY
Sbjct: 13 VRYHNLKAKKYDLCPSCY 30
>gnl|CDD|200526 cd11265, Sema_5C, The Sema domain, a protein interacting module, of
semaphorin 5C (sema5C). In Drosophila, Sema5C was
identified as an early development gene, which is
expressed in stage 2 embryos with a striped pattern
emerging at later stages. Sema5c may play a role in
odor-guided behavior and in tumorigenesis. Sema5C
belongs to class 5 semaphorin family of proteins, which
are transmembrane glycoproteins characterized by unique
thrombospondin specific repeats in the extracellular
region of the protein. Semaphorins are regulatory
molecules involved in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 433
Score = 30.5 bits (69), Expect = 1.9
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 280 IVHRVTEQTLVRVRFENCDNKWTFDPRALTKVDPFVAGDFVYFIPDELSAKEHL 333
I + +R + ++KW +P+ V F G+FVYF+ E SA E++
Sbjct: 145 IYRTLGTSNKSFLRTKQYNSKWLNEPQF---VGSFETGNFVYFLFRE-SAVEYM 194
>gnl|CDD|215250 PLN02456, PLN02456, citrate synthase.
Length = 455
Score = 30.4 bits (69), Expect = 2.3
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 11/59 (18%)
Query: 156 GLNWEWENQDGGPGKTGRIISIEDGKVGK-------SYRSVAKVLWSI----GKENIYR 203
G ++E + GP + R+ I+ GK YR+ A VL I G E I R
Sbjct: 31 GKDYESPLSELGPVQAERLKKIKAGKDDLGLKTVDPGYRNTAPVLSEISLIDGDEGILR 89
>gnl|CDD|237478 PRK13709, PRK13709, conjugal transfer nickase/helicase TraI;
Provisional.
Length = 1747
Score = 30.1 bits (68), Expect = 2.8
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 10/55 (18%)
Query: 405 NSQVNASTQSAP--LLNSESPPDVVEEVEAVMREVVRGNP---SAVKAFLENNAN 454
Q+ A P L+ + S DV A+M+E+VR P AV + + +
Sbjct: 1099 TDQLQAIAPGQPFRLMQTRSAADV-----AIMKEIVRQTPELREAVYSLINRDVE 1148
>gnl|CDD|216750 pfam01869, BcrAD_BadFG, BadF/BadG/BcrA/BcrD ATPase family. This
family includes the BadF and BadG proteins that are two
subunits of Benzoyl-CoA reductase, that may be involved
in ATP hydrolysis. The family also includes an activase
subunit from the enzyme 2-hydroxyglutaryl-CoA
dehydratase. An uncharacterized protein from Aquifex
aeolicus contains two copies of this region suggesting
that the family may structurally dimerise. This family
appears to be related to pfam00370.
Length = 257
Score = 29.7 bits (67), Expect = 2.9
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 165 DGGPGKTGRIISIEDGKVGKSYRSVAKVLWSIGKEN 200
DGG KT ++ EDG+V S + + S+G E
Sbjct: 3 DGGSTKTKAVLMDEDGEVLGRAISGSANIESVGVEA 38
>gnl|CDD|239902 cd04455, S1_NusA, S1_NusA: N-utilizing substance A protein (NusA),
S1-like RNA-binding domain. S1-like RNA-binding domains
are found in a wide variety of RNA-associated proteins.
NusA is a transcription elongation factor containing an
N-terminal catalytic domain and three RNA binding
domains (RBD's). The RBD's include one S1 domain and two
KH domains that form an RNA binding surface. DNA
transcription by RNA polymerase (RNAP) includes three
phases - initiation, elongation, and termination. During
initiation, sigma factors bind RNAP and target RNAP to
specific promoters. During elongation, N-utilization
substances (NusA, B, E, and G) replace sigma factors and
regulate pausing, termination, and antitermination. NusA
is cold-shock-inducible.
Length = 67
Score = 27.0 bits (61), Expect = 3.5
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 8/32 (25%)
Query: 241 FRRGDRVKVITDAKTLQHVQESSKGGWTPQLL 272
+R GDR+K + V+++SKG PQ++
Sbjct: 41 YRPGDRIKAY-----VLEVRKTSKG---PQII 64
>gnl|CDD|233980 TIGR02712, urea_carbox, urea carboxylase. Members of this family
are ATP-dependent urea carboxylase, including
characterized members from Oleomonas sagaranensis (alpha
class Proteobacterium) and yeasts such as Saccharomyces
cerevisiae. The allophanate hydrolase domain of the
yeast enzyme is not included in this model and is
represented by an adjacent gene in Oleomonas
sagaranensis. The fusion of urea carboxylase and
allophanate hydrolase is designated urea amidolyase. The
enzyme from Oleomonas sagaranensis was shown to be
highly active on acetamide and formamide as well as urea
[Central intermediary metabolism, Nitrogen metabolism].
Length = 1201
Score = 29.6 bits (67), Expect = 3.9
Identities = 13/22 (59%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 7 GLRVIRGPDWKWLDEDGGEGGL 28
G+R+I GP KW DGGE GL
Sbjct: 666 GVRLI-GPKPKWARSDGGEAGL 686
>gnl|CDD|116452 pfam07840, FadR_C, FadR C-terminal domain. This family contains
sequences that are similar to the fatty acid metabolism
regulator protein (FadR). This functions as a dimer,
with each monomer being composed of an N-terminal
DNA-binding domain and a regulatory C-terminal domain. A
linker comprising two short alpha helices joins the two
domains. In the C-terminal domain, an antiparallel array
of six alpha helices forms a barrel-like structure,
while a seventh alpha helix forms a 'lid' at the end
closest to the N-terminal domain. This structure was
found to be similar to that of the C-terminal domain of
the Tet repressor. Long-chain acyl-CoA thioesters
interact directly and reversibly with the C-terminal
domain, and this interaction affects the structure and
therefore the DNA binding properties of the N-terminal
domain.
Length = 164
Score = 28.3 bits (64), Expect = 6.1
Identities = 9/50 (18%), Positives = 19/50 (38%), Gaps = 8/50 (16%)
Query: 418 LNSESPPDVVEEVEAV--------MREVVRGNPSAVKAFLENNANLIDCP 459
L+ + PD+++ + + +R ++ NP L L D
Sbjct: 18 LDEDGVPDLIDNLLSARTNISAIYIRAAIKNNPEKSAEILAQLDELEDTA 67
>gnl|CDD|203523 pfam06815, RVT_connect, Reverse transcriptase connection domain.
This domain is known as the connection domain. This
domain lies between the thumb and palm domains.
Length = 102
Score = 27.2 bits (61), Expect = 6.4
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 164 QDGGPGKTGRIISIEDGKVGKSYRSVAKVLWSIGKENIYRIG 205
Q+ P KTG+ + + R +A+ + IGKE+I G
Sbjct: 27 QEKKPLKTGKYAKQK-NAHTNTVRQLAEAVQKIGKESIVIWG 67
>gnl|CDD|197913 smart00845, GatB_Yqey, GatB domain. This domain is found in GatB
and proteins related to bacterial Yqey. It is about 140
amino acid residues long. This domain is found at the C
terminus of GatB which transamidates Glu-tRNA to
Gln-tRNA. The function of this domain is uncertain. It
does however suggest that Yqey and its relatives have a
role in tRNA metabolism.
Length = 147
Score = 27.9 bits (63), Expect = 6.7
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 11/51 (21%)
Query: 417 LLNSESPPDVVEE-----------VEAVMREVVRGNPSAVKAFLENNANLI 456
L +SP ++VEE +EA++ EV+ NP AV+ + +
Sbjct: 69 LEGGKSPEEIVEEKGLKQISDEGELEAIVDEVIAENPDAVEDYRAGKKKAL 119
>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated.
Length = 470
Score = 28.7 bits (65), Expect = 8.5
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 8/32 (25%)
Query: 241 FRRGDRVKVITDAKTLQHVQESSKGGWTPQLL 272
FR GDRV+ + V++ ++G PQ++
Sbjct: 172 FRPGDRVRAY-----VYEVRKEARG---PQII 195
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 0.136 0.415
Gapped
Lambda K H
0.267 0.0833 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,302,365
Number of extensions: 2208319
Number of successful extensions: 2049
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2047
Number of HSP's successfully gapped: 36
Length of query: 464
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 364
Effective length of database: 6,502,202
Effective search space: 2366801528
Effective search space used: 2366801528
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: 61 (27.1 bits)