RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8644
(173 letters)
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain. Cadherins
are glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium. They
play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing proteins
exist as monomers, homodimers, or heterodimers.
Length = 98
Score = 48.1 bits (115), Expect = 6e-08
Identities = 16/33 (48%), Positives = 23/33 (69%)
Query: 111 QYSLSIPEDVPVGTVVQVVSASDADLGVNSKLS 143
Y +S+PE+ P GTVV VSA+D D G N +++
Sbjct: 1 SYEVSVPENAPPGTVVLTVSATDPDSGENGEVT 33
Score = 27.7 bits (62), Expect = 1.2
Identities = 14/47 (29%), Positives = 16/47 (34%), Gaps = 6/47 (12%)
Query: 60 TLKRAL---RTEEHWLKVENTKHKGSNPGPLVGTCNTTIIVEDQNDN 103
T + L + L V PL T TI V D NDN
Sbjct: 55 TTAKPLDREEQSSYTLTVT---ATDGGGPPLSSTATVTITVLDVNDN 98
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 47.3 bits (113), Expect = 8e-08
Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 7/61 (11%)
Query: 112 YSLSIPEDVPVGTVVQVVSASDADLGVNSKLSWNELE--PNGLFSSD-----LRVEWVIN 164
YS S+PE+ PVGT V V+A+DADLG N ++ ++ L P G F D L ++
Sbjct: 1 YSASVPENAPVGTEVLTVTATDADLGPNGRIFYSILGGGPGGWFRIDPDTGDLSTTKPLD 60
Query: 165 R 165
R
Sbjct: 61 R 61
>gnl|CDD|214520 smart00112, CA, Cadherin repeats. Cadherins are glycoproteins
involved in Ca2+-mediated cell-cell adhesion. Cadherin
domains occur as repeats in the extracellular regions
which are thought to mediate cell-cell contact when
bound to calcium.
Length = 81
Score = 30.0 bits (68), Expect = 0.17
Identities = 24/73 (32%), Positives = 28/73 (38%), Gaps = 10/73 (13%)
Query: 39 FTFSIA------KFIANPTTRLYKNVGTLKRALRTEEHWLKVENTKHKGSNPGPLVGTCN 92
T+SI F +P T L R + E+ L VE T PL T
Sbjct: 13 VTYSILSGNDDGLFSIDPETGEITTTKPLDREEQ-PEYTLTVEATDG---GGPPLSSTAT 68
Query: 93 TTIIVEDQNDNNP 105
TI V D NDN P
Sbjct: 69 VTITVLDVNDNAP 81
>gnl|CDD|234302 TIGR03664, fut_nucase, futalosine nucleosidase. This enzyme
catalyzes the conversion of futalosine to
de-hypoxanthine futalosine in a pathway for the
biosynthesis of menaquinone distinct from the pathway
observed in E. coli.
Length = 222
Score = 31.2 bits (71), Expect = 0.20
Identities = 14/51 (27%), Positives = 17/51 (33%)
Query: 115 SIPEDVPVGTVVQVVSASDADLGVNSKLSWNELEPNGLFSSDLRVEWVINR 165
P VG +V S ADLG + + LE G D N
Sbjct: 67 GFPGSAAVGDLVVATSEIAADLGAETPEGFLPLEALGFPVLDRGGSSYFNS 117
>gnl|CDD|172630 PRK14141, PRK14141, heat shock protein GrpE; Provisional.
Length = 209
Score = 30.0 bits (68), Expect = 0.47
Identities = 10/13 (76%), Positives = 10/13 (76%)
Query: 119 DVPVGTVVQVVSA 131
DVP TVVQVV A
Sbjct: 161 DVPNNTVVQVVQA 173
>gnl|CDD|234804 PRK00629, pheT, phenylalanyl-tRNA synthetase subunit beta;
Reviewed.
Length = 791
Score = 29.8 bits (68), Expect = 0.79
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 105 PIFPVSQ--YSLSIPEDVPVGTVVQVVSASDADL 136
FP + +L + EDVP +++ + + L
Sbjct: 697 SKFPAVRRDLALVVDEDVPAADILKAIKKAGGKL 730
>gnl|CDD|202554 pfam03147, FDX-ACB, Ferredoxin-fold anticodon binding domain. This
is the anticodon binding domain found in some
phenylalanyl tRNA synthetases. The domain has a
ferredoxin fold.
Length = 94
Score = 26.7 bits (60), Expect = 3.2
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 105 PIFPVSQ--YSLSIPEDVPVGTVVQVVSASDADL 136
FP + + + EDVP ++ V+ + +L
Sbjct: 1 SKFPAVRRDLAFVVDEDVPAADILDVIRKAGGEL 34
>gnl|CDD|214893 smart00896, FDX-ACB, Ferredoxin-fold anticodon binding domain.
This is the anticodon binding domain found in some
phenylalanyl tRNA synthetases. The domain has a
ferredoxin fold, consisting of an alpha+beta sandwich
with anti-parallel beta-sheets (beta-alpha-beta x2).
Length = 93
Score = 26.6 bits (60), Expect = 3.4
Identities = 8/34 (23%), Positives = 15/34 (44%), Gaps = 2/34 (5%)
Query: 105 PIFPVSQ--YSLSIPEDVPVGTVVQVVSASDADL 136
FP + + + EDVP ++ + + DL
Sbjct: 1 SKFPAVRRDLAFVVDEDVPAAELLDAIREAGGDL 34
>gnl|CDD|234819 PRK00711, PRK00711, D-amino acid dehydrogenase small subunit;
Validated.
Length = 416
Score = 27.5 bits (62), Expect = 3.7
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 4/25 (16%)
Query: 105 PIFPVSQYSLSIP---EDV-PVGTV 125
P++P+ YSL++P ED PV TV
Sbjct: 269 PVYPLKGYSLTVPITDEDRAPVSTV 293
>gnl|CDD|218352 pfam04962, KduI, KduI/IolB family. This family includes the 5-keto
4-deoxyuronate isomerase enzyme EC:5.3.1.17 that is
involved in pectin degradation. This family aldo
includes bacterial Myo-inositol catabolism (IolB)
proteins. The Bacillus subtilis inositol operon
(iolABCDEFGHIJ) is involved in myo-inositol catabolism.
Glucose repression of the iol operon induced by inositol
is exerted through catabolite repression mediated by
CcpA and the iol induction system mediated by IolR. The
exact function of IolB is unknown. Members of this
family possess a Cupin like structure.
Length = 261
Score = 27.2 bits (61), Expect = 4.4
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 120 VPVGTVVQVVSASDADLGVNSKLSWNELEPNGLFSSDLRVE 160
VP G V + + +DA++ V S + P + D+ VE
Sbjct: 86 VPKGARVTITALTDAEVAVCSAPADGTFPPRLIAPEDVPVE 126
>gnl|CDD|220030 pfam08817, YukD, WXG100 protein secretion system (Wss), protein
YukD. The YukD protein family members participate in
the formation of a translocon required for the secretion
of WXG100 proteins (pfam06013) in monoderm bacteria,
with the WXG100 protein secretion system (Wss). Like the
cytoplasmic protein EsaC in Staphylococcus aureus, YukD
was hypothesized to play a role of a chaperone. YukD
adopts a ubiquitin-like fold. Usually, ubiquitin
covalently binds to protein and flags them for protein
degradation, however conjugation assays have indicated
that the classical YukD lacks the capacity for covalent
bond formation with other proteins. In contrast to the
situation in firmicutes, YukD-like proteins in
actinobacteria are often fused to a transporter involved
in the ESAT-6/ESX/Wss secretion pathway. Members of the
YukD family are also associated in gene neighborhoods
with other enzymatic members of the ubiquitin signaling
and degradation pathway such as the E1, E2 and E3
trienzyme complex that catalyze ubiquitin transfer to
substrates, and the JAB family metallopeptidases that
are involved in its release. This suggests that a subset
of the YukD family in bacteria are conjugated and
released from proteins as in the eukaryotic
ubiquitin-mediated signaling and degradation pathway.
Length = 77
Score = 25.7 bits (57), Expect = 5.4
Identities = 9/32 (28%), Positives = 13/32 (40%), Gaps = 4/32 (12%)
Query: 108 PVSQYSLSIPEDVPVGT----VVQVVSASDAD 135
Q L +P DVPV +V+ + D
Sbjct: 10 HGRQVDLVLPADVPVKELIPLLVEALKLPGTD 41
>gnl|CDD|187858 cd09727, Cas6_I-E, CRISPR/Cas system-associated RAMP superfamily
protein Cas6e. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas6e is an endoribonuclease that generates crRNA; This
family is specific for CRISPR/Cas system I-E subtype;
Homologous to Cas6 (RAMP superfamily protein); Possesses
double RRM/ferredoxin fold; also known as Cse3 family.
Length = 210
Score = 26.5 bits (59), Expect = 6.5
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 6/56 (10%)
Query: 21 LESRYLHLRPKSGMYAPAFTFSIAKFIANPTTRLYKNVGTLKRALRTEEHWLKVEN 76
++++ K+G F + ANPT RL KR + L E
Sbjct: 79 VQTKPFDPALKAGQR---LRFRL---RANPTRRLNGKRKDRKRRPDGKRVALLREQ 128
>gnl|CDD|223150 COG0072, PheT, Phenylalanyl-tRNA synthetase beta subunit
[Translation, ribosomal structure and biogenesis].
Length = 650
Score = 26.5 bits (59), Expect = 8.4
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 105 PIFP-VSQ-YSLSIPEDVPVGTVVQVVSASDADL 136
FP V + +L + EDVP G +V+ + + L
Sbjct: 558 SKFPAVRRDIALVVDEDVPAGDIVKAIKKAGGKL 591
>gnl|CDD|182223 PRK10073, PRK10073, putative glycosyl transferase; Provisional.
Length = 328
Score = 26.2 bits (58), Expect = 9.2
Identities = 5/21 (23%), Positives = 6/21 (28%)
Query: 88 VGTCNTTIIVEDQNDNNPIFP 108
V CN D + P
Sbjct: 117 VAQCNADWCFRDTGETWQSIP 137
>gnl|CDD|235848 PRK06664, fliD, flagellar hook-associated protein FliD; Validated.
Length = 661
Score = 26.7 bits (59), Expect = 9.2
Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 12/79 (15%)
Query: 93 TTIIVEDQNDNNPIF---------PVSQYSLSIPEDVPV--GTVVQVVSASDADLGVNSK 141
I+ + N +F P+S+ S+ IPE + + + ++ S D
Sbjct: 214 QPIVYGQSSSTNKLFFTENGIVLEPLSEQSIDIPETIEIKKRSKIEFE-VSYEDASEEEI 272
Query: 142 LSWNELEPNGLFSSDLRVE 160
+ P +VE
Sbjct: 273 ENKIVFNPGEATFEGAKVE 291
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 0.132 0.398
Gapped
Lambda K H
0.267 0.0879 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,608,679
Number of extensions: 751431
Number of successful extensions: 410
Number of sequences better than 10.0: 1
Number of HSP's gapped: 410
Number of HSP's successfully gapped: 19
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
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: 42 (22.0 bits)
S2: 55 (24.7 bits)