RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9843
(175 letters)
>gnl|CDD|153402 cd08033, LARP_6, La RNA-binding domain of La-related protein 6.
This domain is found in animal and plant proteins
related to the La autoantigen. A variety of La-related
proteins (LARPs or La ribonucleoproteins), with
differing domain architecture, appear to function as
RNA-binding proteins in eukaryotic cellular processes.
Length = 77
Score = 130 bits (329), Expect = 3e-40
Identities = 50/77 (64%), Positives = 67/77 (87%)
Query: 35 TKRIIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAFAL 94
++I+ QVE+YFSDEN++KDAFLLKHV+RNKEG+V +KLI+SFK+VK L++DWRVVA AL
Sbjct: 1 IQKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAAL 60
Query: 95 AKSEKLQINEQGTKIRR 111
+S KL ++E G K+RR
Sbjct: 61 RRSSKLVVSEDGKKVRR 77
>gnl|CDD|128955 smart00715, LA, Domain in the RNA-binding Lupus La protein; unknown
function.
Length = 80
Score = 106 bits (266), Expect = 1e-30
Identities = 38/80 (47%), Positives = 57/80 (71%), Gaps = 1/80 (1%)
Query: 32 EDLTKRIIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVA 91
E+L ++I QVE+YFSDEN+ +D FL K + +N +G+V + I+SFKRVK L+ D ++
Sbjct: 1 EELKQKIKKQVEYYFSDENLPRDKFLRKKMDKN-DGYVPISTIASFKRVKSLTTDVNLIV 59
Query: 92 FALAKSEKLQINEQGTKIRR 111
AL S KL+++E G K+RR
Sbjct: 60 EALRSSPKLEVSEDGLKVRR 79
>gnl|CDD|153396 cd07323, LAM, LA motif RNA-binding domain. This domain is found at
the N-terminus of La RNA-binding proteins as well as in
other related proteins. Typically, the domain co-occurs
with an RNA-recognition motif (RRM), and together these
domains function to bind primary transcripts of RNA
polymerase III in the La autoantigen (Lupus La protein,
LARP3, or Sjoegren syndrome type B antigen, SS-B). A
variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain architecture,
appear to function as RNA-binding proteins in eukaryotic
cellular processes.
Length = 75
Score = 93.4 bits (233), Expect = 1e-25
Identities = 34/76 (44%), Positives = 52/76 (68%), Gaps = 2/76 (2%)
Query: 36 KRIIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAFALA 95
++I QVE+YFSDEN+ KD FL + + +G+V L L++SF RVK L+ D ++ AL
Sbjct: 2 EKIKKQVEYYFSDENLCKDRFLRSLM--DDDGWVPLSLLASFNRVKKLTTDVELILEALR 59
Query: 96 KSEKLQINEQGTKIRR 111
S ++++E GTK+RR
Sbjct: 60 DSSVVEVSEDGTKVRR 75
>gnl|CDD|203243 pfam05383, La, La domain. This presumed domain is found at the
N-terminus of La RNA-binding proteins as well as other
proteins. The function of this region is uncertain.
Length = 59
Score = 80.7 bits (200), Expect = 5e-21
Identities = 27/60 (45%), Positives = 40/60 (66%), Gaps = 1/60 (1%)
Query: 38 IIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAFALAKS 97
I QVE+YFSDEN+ +D FL K + ++ G+V + I+SFKR+K L+ D ++ AL S
Sbjct: 1 IKKQVEYYFSDENLPRDKFLRKQMDKD-PGYVPISTIASFKRIKKLTTDVNLIVEALRSS 59
>gnl|CDD|153398 cd08029, LA_like_fungal, La-motif domain of fungal proteins similar
to the La autoantigen. This domain is found in fungal
proteins related to the La autoantigen. A variety of
La-related proteins (LARPs or La ribonucleoproteins),
with differing domain architecture, appear to function
as RNA-binding proteins in eukaryotic cellular
processes.
Length = 76
Score = 71.2 bits (175), Expect = 5e-17
Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 37 RIIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAFALAK 96
I QVEFYFSD N+ D FL + G+V +K I+SFKR++ + V AL +
Sbjct: 3 EIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRF-QPLEAVVEALRE 61
Query: 97 SEKLQINEQGTKIRR 111
SE L+++E G +RR
Sbjct: 62 SELLEVSEDGENVRR 76
>gnl|CDD|153397 cd08028, LARP_3, La RNA-binding domain of La-related protein 3.
This domain is found at the N-terminus of the La
autoantigen and similar proteins, and co-occurs with an
RNA-recognition motif (RRM). Together these domains
function to bind primary transcripts of RNA polymerase
III at their 3' terminus and protect them from
exonucleolytic degradation. Binding is specific for the
3'-terminal UUU-OH motif. The La autoantigen is also
called Lupus La protein, LARP3, or Sjoegren syndrome
type B antigen (SS-B).
Length = 82
Score = 70.8 bits (174), Expect = 7e-17
Identities = 35/81 (43%), Positives = 56/81 (69%), Gaps = 3/81 (3%)
Query: 33 DLTKRIIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAF 92
DL K+II Q+E+YF D N+ +D FL + +K + +G+V ++++ F R+K LS D V+A
Sbjct: 3 DLEKKIIRQIEYYFGDFNLPRDKFLKEQIKED-DGWVPMEVMLKFNRLKSLSSDPEVIAK 61
Query: 93 ALAKSEK--LQINEQGTKIRR 111
AL KS+ ++++E TKIRR
Sbjct: 62 ALKKSKSGLIEVSEDKTKIRR 82
>gnl|CDD|153399 cd08030, LA_like_plant, La-motif domain of plant proteins similar
to the La autoantigen. This domain is found in plant
proteins related to the La autoantigen. A variety of
La-related proteins (LARPs or La ribonucleoproteins),
with differing domain architecture, appear to function
as RNA-binding proteins in eukaryotic cellular
processes.
Length = 90
Score = 70.1 bits (172), Expect = 2e-16
Identities = 35/90 (38%), Positives = 52/90 (57%), Gaps = 12/90 (13%)
Query: 34 LTKRIIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHL-----SKDWR 88
++++ QVEFYFSD N+ +D FLL+ V+ + +G VSL LI SF R++ L K
Sbjct: 1 TKEKVLRQVEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPED 60
Query: 89 V-------VAFALAKSEKLQINEQGTKIRR 111
V VA AL S L+++E G ++ R
Sbjct: 61 VPEDTLKAVAEALRTSTLLKVSEDGKRVGR 90
>gnl|CDD|153401 cd08032, LARP_7, La RNA-binding domain of La-related protein 7.
LARP7 is a component of the 7SK snRNP, a key factor in
the regulation of RNA polymerase II transcription. 7SK
functionality is dependent on the presence of LARP7,
which is thought to stabilize the 7SK RNA by interacting
with its 3' end. The release of 7SK RNA from
P-TEFb/HEXIM/7SK complexes activates the
cyclin-dependent kinase P-TEFb, which in turn
phosphorylates the C-terminal domain of RNA pol II and
mediates a transition into productive transcription
elongation.
Length = 82
Score = 67.7 bits (165), Expect = 2e-15
Identities = 28/74 (37%), Positives = 53/74 (71%)
Query: 38 IIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAFALAKS 97
I QV+F+F D N+ KD FL + ++++++G++ + L+ SF ++K L+ D +++A AL S
Sbjct: 9 IAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNS 68
Query: 98 EKLQINEQGTKIRR 111
+++N +GT+IRR
Sbjct: 69 SVVELNLEGTRIRR 82
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La) family.
It is expressed predominantly in neurons and muscle in
vertebrates. LARP6 functions as a key regulatory protein
that may play a role in mediating a variety of
developmental and homeostatic processes in animals,
including myogenesis, neurogenesis and possibly
metastasis. LARP6 binds to Ca2+/calmodulin-dependent
serine protein kinase (CASK), and forms a complex with
inhibitor of differentiation transcription factors. It
is structurally related to the La autoantigen and
contains a La motif (LAM), nuclear localization and
export (NLS and NES) signals, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 66.1 bits (162), Expect = 7e-15
Identities = 25/47 (53%), Positives = 33/47 (70%)
Query: 125 RTIVAINIPPESATIELVAEMFKPCGEIALIRLLRPGKYTKYGNTRH 171
RT+VA+N+P E +TIE V E+F CG IALIR+LRPG+ R+
Sbjct: 1 RTVVAVNLPEEESTIESVLELFSTCGVIALIRILRPGRTIPPDLKRY 47
>gnl|CDD|153403 cd08034, LARP_1_2, La RNA-binding domain proteins similar to
La-related proteins 1 and 2. This domain is found in
proteins similar to vertebrate La-related proteins 1 and
2 (LARP1, LARP2). A variety of La-related proteins
(LARPs or La ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding proteins
in eukaryotic cellular processes.
Length = 73
Score = 64.8 bits (158), Expect = 2e-14
Identities = 27/74 (36%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 38 IIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAFALAKS 97
I Q+E+YFS +N+ KD FL + K + EG++ + LI+SF RV+ L+ D ++ AL S
Sbjct: 4 IKKQIEYYFSVDNLEKDFFLRR--KMDPEGYLPIALIASFHRVQALTTDVNLILEALKDS 61
Query: 98 EKLQINEQGTKIRR 111
+++ K+R
Sbjct: 62 TVVELV--DEKVRC 73
>gnl|CDD|153400 cd08031, LARP_4_5_like, La RNA-binding domain of proteins similar
to La-related proteins 4 and 5. This domain is found in
proteins similar to La-related proteins 4 and 5 (LARP4,
LARP5). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain architecture,
appear to function as RNA-binding proteins in eukaryotic
cellular processes.
Length = 75
Score = 55.5 bits (134), Expect = 4e-11
Identities = 25/70 (35%), Positives = 47/70 (67%), Gaps = 2/70 (2%)
Query: 41 QVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAFALAKSEKL 100
Q+E+YFS EN+ DA+LL + + + +V + I++F ++K L+ D ++ AL +S +
Sbjct: 7 QLEYYFSRENLANDAYLLSQM--DSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNV 64
Query: 101 QINEQGTKIR 110
Q++E+G K+R
Sbjct: 65 QVDEKGEKVR 74
>gnl|CDD|153407 cd08038, LARP_2, La RNA-binding domain of La-related protein 2.
This domain is found in vertebrate La-related protein 2
(LARP2). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain architecture,
appear to function as RNA-binding proteins in eukaryotic
cellular processes.
Length = 73
Score = 51.5 bits (123), Expect = 2e-09
Identities = 28/71 (39%), Positives = 47/71 (66%), Gaps = 4/71 (5%)
Query: 41 QVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAFALAKSEKL 100
Q+E+YFS EN+ +D FL + K + +GF+ + LI+ F RV+ L+ + ++ AL S ++
Sbjct: 7 QIEYYFSTENLERDFFLRR--KMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDSTEV 64
Query: 101 QINEQGTKIRR 111
+I +Q KIRR
Sbjct: 65 EIVDQ--KIRR 73
>gnl|CDD|153406 cd08037, LARP_1, La RNA-binding domain of La-related protein 1.
This domain is found in vertebrate La-related protein 1
(LARP1). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain architecture,
appear to function as RNA-binding proteins in eukaryotic
cellular processes.
Length = 73
Score = 50.3 bits (120), Expect = 5e-09
Identities = 31/80 (38%), Positives = 52/80 (65%), Gaps = 7/80 (8%)
Query: 32 EDLTKRIIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVA 91
+D KR Q+E+YFS +N+ +D FL + K +++GF+ + LI+SF RV+ L+ D ++
Sbjct: 1 KDYIKR---QIEYYFSVDNLERDFFLRR--KMDEDGFLPVTLIASFHRVQALTTDISLII 55
Query: 92 FALAKSEKLQINEQGTKIRR 111
AL S+ ++I + KIRR
Sbjct: 56 KALKDSKVVEIIDM--KIRR 73
>gnl|CDD|153404 cd08035, LARP_4, La RNA-binding domain of La-related protein 4.
This domain is found in vertebrate La-related protein 4
(LARP4), also known as c-MPL binding protein. La-type
domains often co-occur with RNA-recognition motifs
(RRMs). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain architecture,
appear to function as RNA-binding proteins in eukaryotic
cellular processes.
Length = 75
Score = 42.3 bits (99), Expect = 5e-06
Identities = 22/70 (31%), Positives = 42/70 (60%), Gaps = 2/70 (2%)
Query: 41 QVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAFALAKSEKL 100
Q+EF FS EN+ KD +L+ + + + FV + +++ + +K L+ D ++ L S +
Sbjct: 7 QLEFCFSRENLSKDLYLISQM--DSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMV 64
Query: 101 QINEQGTKIR 110
Q++E G K+R
Sbjct: 65 QVDETGEKVR 74
>gnl|CDD|227520 COG5193, LHP1, La protein, small RNA-binding pol III transcript
stabilizing protein and related La-motif-containing
proteins involved in translation [Posttranslational
modification, protein turnover, chaperones /
Translation, ribosomal structure and biogenesis].
Length = 438
Score = 40.4 bits (94), Expect = 2e-04
Identities = 22/59 (37%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 28 VKPDEDLTKRIIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKD 86
V+P +Q+E+YFS+EN+ D FL K K K GF+ L I F R D
Sbjct: 264 VEPILLSIMAKKEQIEYYFSEENLKSDEFLRKKFK--KAGFIPLSFIGKFYRNLSFGGD 320
Score = 31.9 bits (72), Expect = 0.13
Identities = 31/95 (32%), Positives = 49/95 (51%), Gaps = 10/95 (10%)
Query: 35 TKRIIDQVEFYFS-----DENIVKDAFLLKHVKRN--KEGFVSLKLISSFKRVKHLSKDW 87
TK + QVEFYFS D N KD FL +N ++ +V +K I++F R+K+
Sbjct: 72 TKWTLKQVEFYFSGSKDTDSNFPKDKFLKTTAPKNKKRDKWVPIKTIATFNRMKNSGSPV 131
Query: 88 RVVAFALAKS---EKLQINEQGTKIRRVDPLPAYD 119
V+ AL KS L+++ G+ R + L + +
Sbjct: 132 SAVSGALRKSLDARVLEVSSSGSNKNRTEKLISNN 166
>gnl|CDD|240734 cd12288, RRM_La_like_plant, RNA recognition motif in plant proteins
related to the La autoantigen. This subfamily
corresponds to the RRM of plant La-like proteins related
to the La autoantigen. A variety of La-related proteins
(LARPs or La ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding proteins
in eukaryotic cellular processes. Members in this family
contain an LAM domain followed by an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 34.4 bits (79), Expect = 0.005
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 125 RTIVAINIPPESATIELVAEMFKPCGEIALIRLLRPGKY 163
RT+VA N+P + +IE + E+F G + +R+ PG+
Sbjct: 1 RTVVAENLPEDH-SIENLEEIFGTVGSVKNVRICDPGRV 38
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface
Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX)
proteins. This subgroup corresponds to the conserved
RNA recognition motif (RRM) in ECTO-NOX proteins (also
termed ENOX), comprising a family of plant and animal
NAD(P)H oxidases exhibiting both, oxidative and protein
disulfide isomerase-like, activities. They are
growth-related and drive cell enlargement, and may play
roles in aging and neurodegenerative diseases. ENOX
proteins function as terminal oxidases of plasma
membrane electron transport (PMET) through catalyzing
electron transport from plasma membrane quinones to
extracellular oxygen, forming water as a product. They
are also hydroquinone oxidases that oxidize externally
supplied NADH, hence NOX. ENOX proteins harbor a
di-copper center that lack flavin. ENOX proteins display
protein disulfide interchange activity that is also
possessed by protein disulfide isomerase. In contrast to
the classic protein disulfide isomerases, ENOX proteins
lack the double CXXC motif. This family includes two
ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed
candidate growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous and
refractory to drugs. ENOX2, also termed APK1 antigen, or
cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role in
cell proliferation and tumor progression. In contrast to
ENOX1, ENOX2 is drug-responsive and harbors a drug
binding site to which the cancer-specific S-peptide
tagged pan-ENOX2 recombinant (scFv) is directed.
Moreover, ENOX2 is specifically inhibited by a variety
of quinone site inhibitors that have anticancer activity
and is unique to the surface of cancer cells. ENOX
proteins contain many functional motifs.
Length = 84
Score = 33.9 bits (78), Expect = 0.007
Identities = 13/24 (54%), Positives = 19/24 (79%)
Query: 134 PESATIELVAEMFKPCGEIALIRL 157
PE+AT E++ E+F+ CGEI IR+
Sbjct: 15 PENATEEIIREVFEQCGEIIAIRM 38
>gnl|CDD|153405 cd08036, LARP_5, La RNA-binding domain of La-related protein 5.
This domain is found in vertebrate La-related protein 5
(LARP5). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain architecture,
appear to function as RNA-binding proteins in eukaryotic
cellular processes.
Length = 75
Score = 33.5 bits (76), Expect = 0.008
Identities = 18/69 (26%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 42 VEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVAFALAKSEKLQ 101
+EF S EN+ D +L+ + ++ +V + +++ +K LS D ++ L +Q
Sbjct: 8 LEFCLSRENLASDMYLISQMDSDQ--YVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQ 65
Query: 102 INEQGTKIR 110
++E+G K+R
Sbjct: 66 VDEKGEKVR 74
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 33.5 bits (77), Expect = 0.009
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 127 IVAINIPPESATIELVAEMFKPCGEIALIRLLRPGKYTKYGNTRHFSF 174
I+ NIP E AT++ + E+F GE+ +RL P K T G+ R F F
Sbjct: 3 ILVRNIPFE-ATVKELRELFSTFGELKTVRL--PKKMTGTGSHRGFGF 47
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 31.5 bits (72), Expect = 0.045
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 125 RTIVAINIPPESATIELVAEMFKPCGEIALIRLL-RPGKYTKYG 167
RTI N+ P T + + E F GE+ +R+ + T+Y
Sbjct: 5 RTIYVGNLDPT-TTADQLLEFFSQAGEVKYVRMAGDETQPTRYA 47
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 30.7 bits (70), Expect = 0.079
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 124 SRTIVAINIPPESATIELVAEMFKPCGEIALIRLLRPGKYTKYGNTRHFSF 174
SR IV N+P + + ++F+ G I ++L KYTK G R F F
Sbjct: 1 SRLIVK-NLPK-GIKEDKLRKLFEAFGTITDVQL----KYTKDGKFRKFGF 45
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 27.9 bits (63), Expect = 0.74
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 134 PESATIELVAEMFKPCGEIALIRLLRPGKYTKYGNTRHF 172
P S + ++F+ GEI IR P ++ TR F
Sbjct: 9 PPSFDQSDIRDLFEQYGEILSIRF--PSL--RFNKTRRF 43
>gnl|CDD|234207 TIGR03434, ADOP, Acidobacterial duplicated orphan permease.
Members of this protein family are found, so far, only
in three species of Acidobacteria, namely Acidobacteria
bacterium Ellin345, Acidobacterium capsulatum ATCC
51196, and Solibacter usitatus Ellin6076, where they
form large paralogous families. Each protein contains
two copies of a domain called the efflux ABC transporter
permease protein (pfam02687). However, unlike other
members of that family (including LolC, FtsX, and MacB),
genes for these proteins are essentially never found
fused or adjacent to ABC transporter ATP-binding protein
(pfam00005) genes. We name this family ADOP, for
Acidobacterial Duplicated Orphan Permease, to reflect
the restricted lineage, internal duplication, lack of
associated ATP-binding cassette proteins, and permease
homology. The function is unknown.
Length = 803
Score = 29.4 bits (67), Expect = 0.96
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 5/33 (15%)
Query: 68 FVSLKLI-----SSFKRVKHLSKDWRVVAFALA 95
+ L+L+ +S R+ +S D RV+ FALA
Sbjct: 341 YWGLRLLLALLPASLPRLAEISLDGRVLLFALA 373
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar proteins.
This subfamily corresponds to the RRM1 of RBM19 and
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 77
Score = 27.6 bits (62), Expect = 0.99
Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 124 SRTIVAINIPPESATIELVAEMFKPCGEIALIRLLRPGKYTKYGNTRHFSF 174
SR IV N+P EL K GEI ++LLR T+ G +R +F
Sbjct: 1 SRLIVK-NLPASLTEAELKEHFSKHGGEITDVKLLR----TEDGKSRRIAF 46
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 27.2 bits (61), Expect = 1.4
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 131 NIPPESATIELVAEMFKPCGEIALIRLLR---PGKYTKYG 167
N+PP T E + E+F G++ +RL+R GK +
Sbjct: 6 NLPP-DTTEEELRELFSKFGKVESVRLVRDKETGKSKGFA 44
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 26.9 bits (60), Expect = 1.9
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 134 PESATIELVAEMFKPCGEIALIRLL 158
P T E + FK G +RLL
Sbjct: 9 PYDTTAEDLLAHFKNAGAPPSVRLL 33
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes including
mRNA and rRNA processing, RNA export, and RNA stability.
This domain is 90 amino acids in length and consists of
a four-stranded beta-sheet packed against two
alpha-helices. RRM usually interacts with ssRNA, but is
also known to interact with ssDNA as well as proteins.
RRM binds a variable number of nucleotides, ranging from
two to eight. The active site includes three aromatic
side-chains located within the conserved RNP1 and RNP2
motifs of the domain. The RRM domain is found in a
variety heterogeneous nuclear ribonucleoproteins
(hnRNPs), proteins implicated in regulation of
alternative splicing, and protein components of small
nuclear ribonucleoproteins (snRNPs).
Length = 72
Score = 26.5 bits (59), Expect = 2.1
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 131 NIPPESATIELVAEMFKPCGEIALIRLLRPGKYTKYG 167
N+PP T E + E+F GEI +R++R G
Sbjct: 5 NLPP-DTTEEDLRELFSKFGEIESVRIVRDKDGKSKG 40
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein
7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S), an
oligopyrimidine-binding protein that binds to the highly
conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK
RNA. LARP7 is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP). It intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. It plays an essential role in the inhibition of
positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
LARP7 contains a La motif (LAM) and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the N-terminal region,
which mediates binding to the U-rich 3' terminus of 7SK
RNA. LARP7 also carries another putative RRM domain at
its C-terminus. .
Length = 80
Score = 26.6 bits (59), Expect = 2.6
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 134 PESATIELVAEMFKPCGEIALIRLLRPGKYTKYGNTRHFSF 174
P++AT E + +F G + + L R Y G+ + F+F
Sbjct: 8 PKNATHEWLKAVFSKYGTVVYVSLPR---YKHTGDIKGFAF 45
>gnl|CDD|226650 COG4187, RocB, Arginine degradation protein (predicted deacylase)
[Amino acid transport and metabolism].
Length = 553
Score = 28.2 bits (63), Expect = 2.6
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 117 AYDQTTPSRTIVAINIPPESATIELVAEMFKPCGEIALIRLLR--PGKYTKYGNTRHFSF 174
+Y+ TP R + N S T + + + K E A + +Y +YG +
Sbjct: 289 SYNVQTPERAWLYFNWLYHSRTAKELFDRLKEEAETAAEEAIETLRDRYEEYGKLVNRPA 348
Query: 175 G 175
G
Sbjct: 349 G 349
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 26.0 bits (58), Expect = 3.2
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 124 SRTIVAINIPPESATIELVAEMFKPCGEI 152
+ T+ NIPPE I + E F G I
Sbjct: 1 NTTLEVRNIPPELNNITKLNEHFSKFGTI 29
>gnl|CDD|177820 PLN02161, PLN02161, beta-amylase.
Length = 531
Score = 27.7 bits (61), Expect = 3.4
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 53 KDAFLLKHVKRNKEGFVSLKLISSFKRVKHLSKDWRVVA-----FALAKSEK 99
K FL + KRN+ F S+ +I FKR + ++K WR VA F++ EK
Sbjct: 28 KSCFLEQSTKRNRNFFRSVSMIPPFKRGRFITK-WRSVAGNSRIFSMDAREK 78
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 26.0 bits (58), Expect = 4.0
Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 5/49 (10%)
Query: 126 TIVAINIPPESATIELVAEMFKPCGEIALIRLLRPGKYTKYGNTRHFSF 174
++ N+P E AT + + E+F P G++ +RL P K+ G+ R F+F
Sbjct: 2 KLIVRNVPFE-ATKKELRELFSPFGQVKSVRL--PKKF--DGSHRGFAF 45
>gnl|CDD|198276 cd10413, SH2_Grb7, Src homology 2 (SH2) domain found in the
growth factor receptor bound, subclass 7 (Grb7)
proteins. The Grb family binds to the epidermal growth
factor receptor (EGFR, erbB1) via their SH2 domains.
Grb7 is part of the Grb7 family of proteins which also
includes Grb10, and Grb14. They are composed of an
N-terminal Proline-rich domain, a Ras Associating-like
(RA) domain, a Pleckstrin Homology (PH) domain, a
phosphotyrosine interaction region (PIR, BPS) and a
C-terminal SH2 domain. The SH2 domains of Grb7, Grb10
and Grb14 preferentially bind to a different RTK. Grb7
binds strongly to the erbB2 receptor, unlike Grb10 and
Grb14 which bind weakly to it. Grb7 family proteins are
phosphorylated on serine/threonine as well as tyrosine
residues. In general SH2 domains are involved in signal
transduction. They typically bind pTyr-containing
ligands via two surface pockets, a pTyr and hydrophobic
binding pocket, allowing proteins with SH2 domains to
localize to tyrosine phosphorylated sites.
Length = 108
Score = 26.0 bits (57), Expect = 6.6
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 9/50 (18%)
Query: 33 DLTKRIIDQVEFYFSDENIVKDAFLLKHVKRNKEGFVSLKLISSFKRVKH 82
+ ++R+I Q + +V FL++ +RN +GFV L L ++VKH
Sbjct: 15 EESQRLIGQ-------QGLVDGVFLVRESQRNPQGFV-LSL-CHLQKVKH 55
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46), belonging
to the Aly/REF family of RNA binding proteins that have
been implicated in coupling transcription with pre-mRNA
splicing and nucleo-cytoplasmic mRNA transport. SKAR is
widely expressed and localizes to the nucleus. It may be
a critical player in the function of S6K1 in cell and
organism growth control by binding the activated,
hyperphosphorylated form of S6K1 but not S6K2.
Furthermore, SKAR functions as a protein partner of the
p50 subunit of DNA polymerase delta. In addition, SKAR
may have particular importance in pancreatic beta cell
size determination and insulin secretion. SKAR contains
a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain).
Length = 69
Score = 25.3 bits (56), Expect = 6.6
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 15/59 (25%)
Query: 126 TIVAINIPPESATIELVAEMFKPCGEIALIRLLRPGK--------------YTKYGNTR 170
+V N+ P S T + + E+F G + RL+RPG KY N
Sbjct: 2 RLVVSNLHP-SVTEDDIVELFSAIGALKRARLVRPGVAEVVYVRKDDALTAIDKYNNRE 59
>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM2 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 82
Score = 25.5 bits (56), Expect = 6.6
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 124 SRTIVAINIPPESATIELVAEMFKPCGEIALIRLL 158
+RTI NI + ++ CGE++ +RLL
Sbjct: 4 ARTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLL 38
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 25.5 bits (55), Expect = 6.8
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 124 SRTIVAINIPPESATIELVAEMFKPCGEIALIRLLR---PGKYTKYG 167
S+T + +N P++ T E + +F GEI +L+R G+ YG
Sbjct: 3 SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYG 49
>gnl|CDD|237664 PRK14294, PRK14294, chaperone protein DnaJ; Provisional.
Length = 366
Score = 26.7 bits (59), Expect = 7.6
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 5 KVPPGCDTSAKPNSRSENEEIPFVKPDEDLTKRI-IDQVEFYFSDENIV 52
K+P G DT ++ R E E P DL + ++ EF+ D N V
Sbjct: 218 KIPAGVDTGSRLRLRGEGEAGVRGGPPGDLYVFLTVEPHEFFERDGNDV 266
>gnl|CDD|239122 cd02657, Peptidase_C19A, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyse bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 305
Score = 26.5 bits (59), Expect = 8.1
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 96 KSEKLQINEQGTKIRRVDPLPAY 118
S L + TK R+ LP Y
Sbjct: 177 HSPTLGRDAIYTKTSRISRLPKY 199
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 25.3 bits (56), Expect = 9.0
Identities = 9/33 (27%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 125 RTIVAINIPPESATIELVAEMFKPCGEIALIRL 157
RT+ N+P + + + ++FK G I +R
Sbjct: 1 RTVFVGNLPL-TTKKKDLKKLFKQFGPIESVRF 32
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to the
RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family
of RNA-binding proteins. This ubiquitously expressed
family of similarly structured proteins predominantly
localizing to the nuclear, includes FUS (also known as
TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1),
TAF15 (also known as hTAFII68 or TAF2N or RPB56), and
Drosophila Cabeza (also known as SARFH). The
corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a degenerate
hexapeptide repeat motif at the N-terminus. The
C-terminal region consists of a conserved nuclear import
and retention signal (C-NLS), a putative zinc-finger
domain, and a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 25.0 bits (55), Expect = 9.7
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 134 PESATIELVAEMFKPCGEIA 153
P+ T + +AE+F G I
Sbjct: 7 PDDVTEDSLAELFGGIGIIK 26
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
0.318 0.135 0.390
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,048,298
Number of extensions: 841528
Number of successful extensions: 783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 768
Number of HSP's successfully gapped: 57
Length of query: 175
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 85
Effective length of database: 6,945,742
Effective search space: 590388070
Effective search space used: 590388070
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: 56 (25.3 bits)