RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781108|ref|YP_003065521.1| von Willebrand factor type A
[Candidatus Liberibacter asiaticus str. psy62]
(398 letters)
>gnl|CDD|29222 cd00198, vWFA, Von Willebrand factor type A (vWA) domain was
originally found in the blood coagulation protein von
Willebrand factor (vWF). Typically, the vWA domain is
made up of approximately 200 amino acid residues folded
into a classic a/b para-rossmann type of fold. The vWA
domain, since its discovery, has drawn great interest
because of its widespread occurrence and its involvement
in a wide variety of important cellular functions. These
include basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains..
Length = 161
Score = 47.6 bits (112), Expect = 6e-06
Identities = 25/162 (15%), Positives = 56/162 (34%), Gaps = 20/162 (12%)
Query: 209 KIDVLIESAGNLVNSIQKAIQEKKNLSVRIGTIAYNIGIVGNQCTPLSNNLNEVKSRLNK 268
K+D E+ LV+S+ + R+G + + + ++ ++
Sbjct: 17 KLDKAKEALKALVSSLSASPPG-----DRVGLVTFGSNARVVLPLTTDTDKADLLEAIDA 71
Query: 269 LNPY--ENTNTYPAMHHAYRELYNEKESSHNTIGSTRLKKFVIFITDGENSGASAYQNTL 326
L TN A+ A L + K + ++ +I +TDGE +
Sbjct: 72 LKKGLGGGTNIGAALRLALELLKSAKRPNA--------RRVIILLTDGEPND-----GPE 118
Query: 327 NTLQICEYMRNAGMKIYSVAVSAPPEGQDLLRKCTDSSGQFF 368
+ +R G+ +Y++ + +L ++G
Sbjct: 119 LLAEAARELRKLGITVYTIGIGDDANEDELKEIADKTTGGAV 160
>gnl|CDD|143873 pfam00092, VWA, von Willebrand factor type A domain.
Length = 177
Score = 46.2 bits (110), Expect = 1e-05
Identities = 29/131 (22%), Positives = 52/131 (39%), Gaps = 14/131 (10%)
Query: 256 SNNLNEVKSRLNKLNPY--ENTNTYPAMHHAYRELYNEKESSHNTIGSTRLKKFVIFITD 313
+ +++ S + + Y TNT A+ +A L+ S N K VI +TD
Sbjct: 58 YKSKDDLLSAVLRNIYYLGGGTNTGKALKYALENLFRSAGSRPNA------PKVVILLTD 111
Query: 314 GENSGASAYQNTLNTLQICEYMRNAGMKIYSVAVSAPPEGQ-DLLRKCTDSSGQFFAVND 372
G+++ L+ R G+ ++ V V E + L+ S G F V D
Sbjct: 112 GKSNDGGLVPAAAAALR-----RKVGIIVFGVGVGDVDEEELRLIASEPCSEGHVFYVTD 166
Query: 373 SRELLESFDKI 383
L + +++
Sbjct: 167 FDALSDIQEEL 177
>gnl|CDD|29243 cd01470, vWA_complement_factors, Complement factors B and C2 are
two critical proteases for complement activation. They
both contain three CCP or Sushi domains, a trypsin-type
serine protease domain and a single VWA domain with a
conserved metal ion dependent adhesion site referred
commonly as the MIDAS motif. Orthologues of these
molecules are found from echinoderms to chordates.
During complement activation, the CCP domains are
cleaved off, resulting in the formation of an active
protease that cleaves and activates complement C3.
Complement C2 is in the classical pathway and complement
B is in the alternative pathway. The interaction of C2
with C4 and of factor B with C3b are both dependent on
Mg2+ binding sites within the VWA domains and the VWA
domain of factor B has been shown to mediate the binding
of C3. This is consistent with the common inferred
function of VWA domains as magnesium-dependent protein
interaction domains..
Length = 198
Score = 37.1 bits (86), Expect = 0.009
Identities = 38/176 (21%), Positives = 67/176 (38%), Gaps = 16/176 (9%)
Query: 220 LVNSIQKAIQEKKNLSVRIGTIAYNIGIVGNQCTPLSNNLNEVKSRLNKLNPYEN----- 274
+ I+K + + I + A + + + SN+ ++V RL N ++
Sbjct: 25 IKTLIEKISSYEVSPRYEIISYASDPKEIVSIRDFNSNDADDVIKRLEDFNYDDHGDKTG 84
Query: 275 TNTYPAMHHAYRELYNEKESSHNTIGSTRLKKFVIFITDGE-NSGASA------YQNTLN 327
TNT A+ Y + EK + TR +I TDG+ N G S +N +
Sbjct: 85 TNTAAALKKVYERMALEKVRNKEAFNETR--HVIILFTDGKSNMGGSPLPTVDKIKNLVY 142
Query: 328 TLQICEYMRNAGMKIYSVAVSAPPEGQDLLRKCTDSSGQ--FFAVNDSRELLESFD 381
+ R + +Y V ++L + + FF + D +L E FD
Sbjct: 143 KNNKSDNPREDYLDVYVFGVGDDVNKEELNDLASKKDNERHFFKLKDYEDLQEVFD 198
>gnl|CDD|34568 COG4961, TadG, Flp pilus assembly protein TadG [Intracellular
trafficking and secretion].
Length = 185
Score = 34.7 bits (79), Expect = 0.042
Identities = 8/49 (16%), Positives = 19/49 (38%)
Query: 1 MTAIIISVCFLFITYAIDLAHIMYIRNQMQSALDAAVLSGCASIVSDRT 49
A++ L + ++ + +Q+A DAA + + +D
Sbjct: 26 EFALVAPPLLLLVFGIVEFGIAFLAKQSLQNAADAAARAAARGLTTDAA 74
>gnl|CDD|29227 cd01454, vWA_norD_type, norD type: Denitrifying bacteria contain
both membrane bound and periplasmic nitrate reductases.
Denitrification plays a major role in completing the
nitrogen cycle by converting nitrate or nitrite to
nitrogen gas. The pathway for microbial denitrification
has been established as NO3- ------> NO2- ------> NO
-------> N2O ---------> N2. This reaction generally
occurs under oxygen limiting conditions. Genetic and
biochemical studies have shown that the first srep of
the biochemical pathway is catalyzed by periplasmic
nitrate reductases. This family is widely present in
proteobacteria and firmicutes. This version of the
domain is also present in some archaeal members. The
function of the vWA domain in this sub-group is not
known. Members of this subgroup have a conserved MIDAS
motif..
Length = 174
Score = 33.4 bits (76), Expect = 0.12
Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 14/94 (14%)
Query: 262 VKSRLNKLNPYENTNTYPAMHHAYRELYNEKESSHNTIGSTRLKKFVIFITDGENSGASA 321
+ RL L+P NT A+ HA L E +K ++ I+DGE +
Sbjct: 71 ARKRLAALSPGGNTRDGAAIRHAAERLLARPEK----------RKILLVISDGEPNDLDY 120
Query: 322 YQN----TLNTLQICEYMRNAGMKIYSVAVSAPP 351
Y+ T + L+ R G++++ + +
Sbjct: 121 YEGNVFATEDALRAVIEARKLGIEVFGITIDRDA 154
>gnl|CDD|29240 cd01467, vWA_BatA_type, VWA BatA type: Von Willebrand factor type A
(vWA) domain was originally found in the blood
coagulation protein von Willebrand factor (vWF).
Typically, the vWA domain is made up of approximately
200 amino acid residues folded into a classic a/b
para-rossmann type of fold. The vWA domain, since its
discovery, has drawn great interest because of its
widespread occurrence and its involvement in a wide
variety of important cellular functions. These include
basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses. In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains. Members of this subgroup are bacterial in
origin. They are typified by the presence of a MIDAS
motif..
Length = 180
Score = 32.1 bits (73), Expect = 0.29
Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 18/86 (20%)
Query: 301 STRLKKFVIFITDGENSGASAYQNTLNTLQICEYMRNAGMKIYSVAVSAPPEGQDLLRKC 360
S ++ ++ +TDGEN+ ++ E +N G++IY++ V
Sbjct: 99 SEAKERVIVLLTDGENNAGE-----IDPATAAELAKNKGVRIYTIGVG------------ 141
Query: 361 TDSSGQFFAVNDSRELLESFDKITDK 386
S + +S +I DK
Sbjct: 142 -KSGSGPKPDGSTILDEDSLVEIADK 166
>gnl|CDD|146347 pfam03662, Glyco_hydro_79n, Glycosyl hydrolase family 79,
N-terminal domain. Family of endo-beta-N-glucuronidase,
or heparanase. Heparan sulfate proteoglycans (HSPGs)
play a key role in the self- assembly, insolubility and
barrier properties of basement membranes and
extracellular matrices. Hence, cleavage of heparan
sulfate (HS) affects the integrity and functional state
of tissues and thereby fundamental normal and
pathological phenomena involving cell migration and
response to changes in the extracellular
micro-environment. Heparanase degrades HS at specific
intra-chain sites. The enzyme is synthesized as a latent
approximately 65 kDa protein that is processed at the
N-terminus into a highly active approximately 50 kDa
form. Experimental evidence suggests that heparanase may
facilitate both tumour cell invasion and
neovascularization, both critical steps in cancer
progression. The enzyme is also involved in cell
migration associated with inflammation and autoimmunity.
Length = 320
Score = 32.0 bits (73), Expect = 0.33
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 219 NLVNSI-QKAIQEKKNLSVRIG-----TIAYNIGIVGNQCTPLSNNLNE 261
+L N I AI+ L +RIG + Y+ G + + C P + N +
Sbjct: 50 DLSNPILLNAIKAFSPLKIRIGGSLQDQVIYDTGDLKSPCAPFTKNSSG 98
>gnl|CDD|36002 KOG0783, KOG0783, KOG0783, Uncharacterized conserved protein,
contains ankyrin and BTB/POZ domains [Function unknown].
Length = 1267
Score = 30.8 bits (69), Expect = 0.66
Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 2/87 (2%)
Query: 122 GLIPSALTNLSLRSTGIIERSSENLAISICMVLDVSRSMEDLYLQKHNDNNNMTSNKYLL 181
G++PS+ + L E+S + +++ + D + + + Q + ++ + + L
Sbjct: 950 GIVPSSNQSDVLSKPDAEEKSPKPNVVNVTSITDTAGA--SVETQNNIESASSGGDPTQL 1007
Query: 182 PPPPKKSFWSKNTTKSKYAPAPAPANR 208
P T K +P P N
Sbjct: 1008 NGPGALQPVEATPTFDKTSPWPNRENL 1034
>gnl|CDD|38022 KOG2811, KOG2811, KOG2811, Uncharacterized conserved protein
[Function unknown].
Length = 420
Score = 30.3 bits (68), Expect = 0.96
Identities = 33/127 (25%), Positives = 46/127 (36%), Gaps = 33/127 (25%)
Query: 48 RTIKDPTTKKDQTSTIFKKQIKKHLKQGSYIRENAGDIAQKAQINITKDKNNPLQYIAES 107
R K D T+ K Q+KKHLK R N+ + K + L YI
Sbjct: 54 REGKRIPCPLDGKHTVVKDQLKKHLK-----RCNS------------RSKESQLIYI--- 93
Query: 108 KAQYEIPTENLFLKGLIPSALTNLSLRSTGIIERSSENLAISICMVLDVS--RSMEDLYL 165
K T+ T+ S I + S E L I IC +DVS S + ++
Sbjct: 94 KKDVNGGTDE-----------TDKIDSSIEISDLSPEELNIWICKEIDVSDGLSTQQKHV 142
Query: 166 QKHNDNN 172
+H
Sbjct: 143 LQHESLL 149
>gnl|CDD|185747 cd09234, V_HD-PTP_like, Protein-interacting V-domain of mammalian
His-Domain type N23 protein tyrosine phosphatase and
related domains. This family contains the V-shaped (V)
domain of mammalian His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23) and related
domains. It belongs to the V_Alix_like superfamily which
includes the V domains of Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, mammalian Alix
(apoptosis-linked gene-2 interacting protein X/ also
known as apoptosis-linked gene-2 interacting protein 1,
AIP1), and related domains. HD_PTP interacts with the
ESCRT (Endosomal Sorting Complexes Required for
Transport) system, and participates in cell migration
and endosomal trafficking. The related Alix V-domain
(belonging to a different family in this superfamily)
contains a binding site, partially conserved in the
superfamily, for the retroviral late assembly (L) domain
YPXnL motif. The Alix V-domain is also a dimerization
domain. In addition to the V-domain, HD_PTP also has an
N-terminal Bro1-like domain, a proline-rich region
(PRR), a catalytically inactive tyrosine phosphatase
domain, and a region containing a PEST motif. Bro1-like
domains bind components of the ESCRT-III complex,
specifically to CHMP4 in the case of HD-PTP. The
Bro1-like domain of HD-PTP can also bind human
immunodeficiency virus type 1 (HIV-1) nucleocapsid.
HD-PTP is encoded by the PTPN23 gene, a tumor suppressor
gene candidate frequently absent in human kidney,
breast, lung, and cervical tumors. This family also
contains Drosophila Myopic, which promotes epidermal
growth factor receptor (EGFR) signaling, and
Caenorhabditis elegans (enhancer of glp-1) EGO-2 which
promotes Notch signaling.
Length = 337
Score = 29.2 bits (66), Expect = 1.9
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 12/58 (20%)
Query: 54 TTKKDQTSTIFKKQIKKHLKQGSYIRENAGDIAQKAQINITKDKNNPLQYIAESKAQY 111
TT +FK+++KKH + + I +N AQ NI L+ + E+ A+Y
Sbjct: 229 TTTGGDMEDLFKEELKKHDQLVNLIEQNL-----AAQENI-------LKALTEANAKY 274
>gnl|CDD|35604 KOG0383, KOG0383, KOG0383, Predicted helicase [General function
prediction only].
Length = 696
Score = 28.0 bits (62), Expect = 4.1
Identities = 21/96 (21%), Positives = 34/96 (35%), Gaps = 5/96 (5%)
Query: 185 PKKSFWSKNTTKSKYAPAPAPANRKIDVLIESAGNLVNSIQKAIQEKKN----LSVRIGT 240
PK S ++ + P+ +ID I + I KN +
Sbjct: 402 PKISEMKTESSAKFHVLLPSYETIEIDQSILFSVQWGLLIVDEAHRLKNKQSKRFRVLTA 461
Query: 241 IAYNIGIVGNQCTPLSNNLNEVKSRLNKLNPYENTN 276
+ ++ TPL NNL E+ + LN L P +
Sbjct: 462 YPIDSKLL-LTGTPLQNNLEELFNLLNFLTPGRFNS 496
>gnl|CDD|29242 cd01469, vWA_integrins_alpha_subunit, Integrins are a class of
adhesion receptors that link the extracellular matrix to
the cytoskeleton and cooperate with growth factor
receptors to promote celll survival, cell cycle
progression and cell migration. Integrins consist of an
alpha and a beta sub-unit. Each sub-unit has a large
extracellular portion, a single transmembrane segment
and a short cytoplasmic domain. The N-terminal domains
of the alpha and beta subunits associate to form the
integrin headpiece, which contains the ligand binding
site, whereas the C-terminal segments traverse the
plasma membrane and mediate interaction with the
cytoskeleton and with signalling proteins.The VWA
domains present in the alpha subunits of integrins seem
to be a chordate specific radiation of the gene family
being found only in vertebrates. They mediate
protein-protein interactions..
Length = 177
Score = 27.9 bits (62), Expect = 4.8
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 275 TNTYPAMHHAYRELYNEKESSHNTIGSTRLKKFVIFITDGENSGAS 320
TNT A+ + EL++E K ++ ITDGE+
Sbjct: 79 TNTATAIQYVVTELFSESNG-----ARKDATKVLVVITDGESHDDP 119
>gnl|CDD|143942 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is
found in proteins involved in a variety of processes
including transcription regulation (e.g., SNF2, STH1,
brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5),
DNA recombination (e.g., RAD54), and chromatin unwinding
(e.g., ISWI) as well as a variety of other proteins with
little functional information (e.g., lodestar, ETL1).
Length = 295
Score = 28.0 bits (63), Expect = 5.0
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 253 TPLSNNLNEVKSRLNKLNP 271
TP+ NNL E+ S LN L P
Sbjct: 156 TPIQNNLAELWSLLNFLRP 174
>gnl|CDD|37044 KOG1833, KOG1833, KOG1833, Nuclear pore complex, gp210 component
[Nuclear structure, Intracellular trafficking,
secretion, and vesicular transport].
Length = 679
Score = 27.7 bits (61), Expect = 5.3
Identities = 12/54 (22%), Positives = 24/54 (44%)
Query: 203 PAPANRKIDVLIESAGNLVNSIQKAIQEKKNLSVRIGTIAYNIGIVGNQCTPLS 256
PAP + +I E G ++ Q +Q ++ +VRI A + + ++
Sbjct: 71 PAPVHGEIQTSNECTGPVIVFSQDEVQIEQLRAVRILAAATRLIVANGMPVYVA 124
>gnl|CDD|33760 COG3980, spsG, Spore coat polysaccharide biosynthesis protein,
predicted glycosyltransferase [Cell envelope biogenesis,
outer membrane].
Length = 318
Score = 27.6 bits (61), Expect = 6.7
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 230 EKKNLSVRIGTIA----YNIGIVGNQCTPLSNNLNEVKSRLNKLNPYENTNTYPAM 281
+ KNL++++ N+ IV P NL + + +N Y +TN +
Sbjct: 169 DPKNLTLKVLAELEQKNVNLHIVVGSSNPTLKNLRKRAEKYPNINLYIDTNDMAEL 224
>gnl|CDD|144422 pfam00817, IMS, impB/mucB/samB family. These proteins are involved
in UV protection.
Length = 148
Score = 27.5 bits (62), Expect = 6.7
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 219 NLVNSIQKAIQEKKNLSVRIGTIAYN 244
L +++AI E+ L+ IG IA N
Sbjct: 115 ELAKRLRRAIAEETGLTCSIG-IAPN 139
>gnl|CDD|38875 KOG3671, KOG3671, KOG3671, Actin regulatory protein
(Wiskott-Aldrich syndrome protein) [Signal transduction
mechanisms, Cytoskeleton].
Length = 569
Score = 27.4 bits (60), Expect = 7.8
Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 166 QKHNDNNNMTSNKYLLPPPPKKSFWSKNTTKSKYAPAPAPANR 208
+ N N N+ L PPPP + + APAP P R
Sbjct: 327 SRRNPGGNQPPNRSL-PPPPPAGGPIPLPAQGRSAPAPPPPRR 368
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.314 0.129 0.359
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,392,487
Number of extensions: 217700
Number of successful extensions: 458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 456
Number of HSP's successfully gapped: 22
Length of query: 398
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 302
Effective length of database: 4,189,273
Effective search space: 1265160446
Effective search space used: 1265160446
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: 58 (26.1 bits)