RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780388|ref|YP_003064801.1| hypothetical protein
CLIBASIA_01365 [Candidatus Liberibacter asiaticus str. psy62]
(458 letters)
>gnl|CDD|29223 cd01450, vWFA_subfamily_ECM, 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 = 52.3 bits (125), Expect = 3e-07
Identities = 35/175 (20%), Positives = 72/175 (41%), Gaps = 24/175 (13%)
Query: 259 VDSS-SLRHVIKKKHLVRDALASVIRSIKKIDNVNDTVRMGATFFNDRVISDPSFS--WG 315
+D S S+ +K V+D + ++ +K+D D R+G ++D V + S +
Sbjct: 7 LDGSESVGPENFEK--VKDFIEKLV---EKLDIGPDKTRVGLVQYSDDVRVEFSLNDYKS 61
Query: 316 VHKLIRTIVKTFAIDENEMGSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLT 375
L++ + + G T A+Q A + + S + K I++LT
Sbjct: 62 KDDLLKAV---KNLKYLGGGGTNTGKALQYALEQLFSESNA-------RENVPKVIIVLT 111
Query: 376 DGENTQDNEEGIAICNKAKSQGIRIMTIAF-SVNKTQQEKARYFLSNCASPNSFF 429
DG + D + K K +GI++ + ++ + + +++C S F
Sbjct: 112 DG-RSDDGGDPKEAAAKLKDEGIKVFVVGVGPADEEELRE----IASCPSERHVF 161
>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 = 49.9 bits (119), Expect = 2e-06
Identities = 40/157 (25%), Positives = 66/157 (42%), Gaps = 27/157 (17%)
Query: 249 LDPSLSEEHFVDSSSLRHVIKKKHLVRDALASVIRSIKKIDNVNDTVRMGATFFNDRVIS 308
+ S+ + FV S L K ++ D + ++ D + V GA F +
Sbjct: 11 VSGSMLAQDFVKPSRLE---AAKEVLSDFIDR-----RENDRIGLVVFAGAAFTQAPLTL 62
Query: 309 DPSFSWGVHKLIRTIVKTFAIDENEMGSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAK 368
D + ++ +++ I G TAI DA+ A + R+KN+ +
Sbjct: 63 D-------RESLKELLEDIKIGLAGQG-TAIGDAIGLA-----------IKRLKNSEAKE 103
Query: 369 KYIVLLTDGENTQDNEEGIAICNKAKSQGIRIMTIAF 405
+ IVLLTDGEN + AK++G+RI TI
Sbjct: 104 RVIVLLTDGENNAGEIDPATAAELAKNKGVRIYTIGV 140
>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 = 7e-06
Identities = 26/142 (18%), Positives = 50/142 (35%), Gaps = 20/142 (14%)
Query: 277 ALASVIRSIKKIDNVNDTVRMGATFFNDRV-----ISDPSFSWGVHKLIRTIVKTFAIDE 331
A ++ + + R+G F ++ + + + I + K
Sbjct: 21 AKEALKALVSSLSASPPGDRVGLVTFGSNARVVLPLTTDTDKADLLEAIDALKKGL---- 76
Query: 332 NEMGSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLTDGENTQDNEEGIAICN 391
G T I A++ A + + S+ A++ I+LLTDGE E
Sbjct: 77 --GGGTNIGAALRLALELLKSAKRPN---------ARRVIILLTDGEPNDGPELLAEAAR 125
Query: 392 KAKSQGIRIMTIAFSVNKTQQE 413
+ + GI + TI + + E
Sbjct: 126 ELRKLGITVYTIGIGDDANEDE 147
>gnl|CDD|143873 pfam00092, VWA, von Willebrand factor type A domain.
Length = 177
Score = 46.6 bits (111), Expect = 2e-05
Identities = 35/187 (18%), Positives = 68/187 (36%), Gaps = 18/187 (9%)
Query: 259 VDSS-SLRHVIKKKHLVRDALASVIRSIKKIDNVNDTVRMGATFFNDRVISDPSFSWGVH 317
+D S S+ V++ + ++ + +D D R+G ++ V ++ FS +
Sbjct: 6 LDGSGSIGE--ANFEKVKEFIKKLV---ENLDIGPDGTRVGLVQYSSDVTTE--FSLNDY 58
Query: 318 KLIRTIVKTFAIDENEM-GSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLTD 376
K ++ + + G T A++ A + + S A K ++LLTD
Sbjct: 59 KSKDDLLSAVLRNIYYLGGGTNTGKALKYALENLFRSAGS-------RPNAPKVVILLTD 111
Query: 377 GENTQDNEEGIAICNKAKSQGIRIMTIAFSVNKTQQEKARYFLSNCASPNSFFEANSTHE 436
G++ A + G I+ V +E+ R S S F
Sbjct: 112 GKSNDGGLVPAAAAALRRKVG--IIVFGVGVGDVDEEELRLIASEPCSEGHVFYVTDFDA 169
Query: 437 LNKIFRD 443
L+ I +
Sbjct: 170 LSDIQEE 176
>gnl|CDD|34568 COG4961, TadG, Flp pilus assembly protein TadG [Intracellular
trafficking and secretion].
Length = 185
Score = 37.8 bits (87), Expect = 0.006
Identities = 20/138 (14%), Positives = 44/138 (31%), Gaps = 6/138 (4%)
Query: 12 KKLIKSCTGHFFIITALLMPVMLGVGGMLVDVVRWSYYEHALKQAAQTAIITASVPLIQS 71
++ + G + AL+ P +L + +V+ A KQ+ Q A A+ +
Sbjct: 13 RRFRRDRRGAAAVEFALVAPPLLLLVFGIVEF---GIAFLA-KQSLQNAADAAARAAARG 68
Query: 72 LEEVSSRAKNSFTFPKQKIEEYLIRNFENNLKKNFTDREVRDIVRDTAVEMNPRKSAYQV 131
L ++ + N ++ N R + + A Q
Sbjct: 69 LTTDAADLDTIQAAATAFLNAIAPANAFLTVQSNTPSRGTVTVTANVA--DATLFDTSQF 126
Query: 132 VLSSRYDLLLNPLSLFLR 149
++S + +N +
Sbjct: 127 TVTSAVTVSINLARGLVL 144
>gnl|CDD|29238 cd01465, vWA_subgroup, VWA subgroup: 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. Not much is known about the function of the VWA
domain in these proteins. The members do have a
conserved MIDAS motif. The biochemical function however
is not known..
Length = 170
Score = 33.6 bits (77), Expect = 0.11
Identities = 31/147 (21%), Positives = 50/147 (34%), Gaps = 27/147 (18%)
Query: 272 HLVRDALASVIRSIKKIDNVNDTVRMGATFFNDRV-ISDPSFSWGVHKLIRTIVKTFAID 330
LV+ AL ++ D + R+ ++ P+ I AID
Sbjct: 19 PLVKSALKLLV------DQLRPDDRLAIVTYDGAAETVLPATPVRDKAAILA-----AID 67
Query: 331 E-NEMGSTAINDAMQTAYDTII-SSNEDEVHRMKNNLEAKKYIVLLTDGENT---QDNEE 385
GSTA +Q Y V+R I+L TDG+ D +E
Sbjct: 68 RLTAGGSTAGGAGIQLGYQEAQKHFVPGGVNR----------ILLATDGDFNVGETDPDE 117
Query: 386 GIAICNKAKSQGIRIMTIAFSVNKTQQ 412
+ + + GI + T+ F N +
Sbjct: 118 LARLVAQKRESGITLSTLGFGDNYNED 144
>gnl|CDD|33968 COG4245, TerY, Uncharacterized protein encoded in toxicity
protection region of plasmid R478, contains von
Willebrand factor (vWF) domain [General function
prediction only].
Length = 207
Score = 31.1 bits (70), Expect = 0.60
Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 6/94 (6%)
Query: 335 GSTAINDAMQTAYDTIISSNEDEVHRMKNNLEA--KKYIVLLTDGENTQDNEEGIAICNK 392
G T + A+ A D I E+ + N + + ++ L+TDGE T D + G A+ +
Sbjct: 77 GGTPLGAALTLALDMI----EERKRKYDANGKGDYRPWVFLITDGEPTDDWQAGAALVFQ 132
Query: 393 AKSQGIRIMTIAFSVNKTQQEKARYFLSNCASPN 426
+ + + + V +
Sbjct: 133 GERRAKSVAAFSVGVQGADNKTLNQITEKVRQFL 166
>gnl|CDD|29229 cd01456, vWA_ywmD_type, VWA ywmD 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. Not much is known about the function of the
members of this subgroup. All members of this subgroup
however have a conserved MIDAS motif. .
Length = 206
Score = 31.1 bits (70), Expect = 0.69
Identities = 26/137 (18%), Positives = 52/137 (37%), Gaps = 10/137 (7%)
Query: 284 SIKKIDNVNDTVRMGATFFNDRVISDPSFSWGVHK--LIRTIVKTFAIDENEMGSTAIND 341
+ + + D R+G F+ + V K L + + + + A+N
Sbjct: 51 LDETANALPDGTRLGLWTFSGDGDNPLDVRVLVPKGCLTAPVNGFPSAQRSAL-DAALN- 108
Query: 342 AMQTA-YDTIISSNEDEVHRMKNNLEAKKYIVLLTDGENTQDNEEGIAICNKAKSQ---- 396
++QT T +++ E + +VL+TDGE+T + AK +
Sbjct: 109 SLQTPTGWTPLAAALAEAAAYVDP-GRVNVVVLITDGEDTCGPDPCEVARELAKRRTPAP 167
Query: 397 GIRIMTIAFSVNKTQQE 413
I++ I F + + E
Sbjct: 168 PIKVNVIDFGGDADRAE 184
>gnl|CDD|34274 COG4655, COG4655, Predicted membrane protein [Function unknown].
Length = 565
Score = 30.7 bits (69), Expect = 0.81
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 7/73 (9%)
Query: 12 KKLIKSCTGHFFIITALLMPVMLGVGGMLVDVVRWSYYEHALKQAAQTAIITASVPLIQS 71
+ +S G ++TAL +P+ L + VD + L++ A A I A+ +
Sbjct: 5 PRRQRSMVG---VLTALFVPLALATLLLGVDYGYLYLEQRELQRVADLAAIAAA----SN 57
Query: 72 LEEVSSRAKNSFT 84
L++ + SFT
Sbjct: 58 LDDAEQAVQTSFT 70
>gnl|CDD|29253 cd01480, vWA_collagen_alpha_1-VI-type, VWA_collagen alpha(VI) type:
The extracellular matrix represents a complex alloy of
variable members of diverse protein families defining
structural integrity and various physiological
functions. The most abundant family is the collagens
with more than 20 different collagen types identified
thus far. Collagens are centrally involved in the
formation of fibrillar and microfibrillar networks of
the extracellular matrix, basement membranes as well as
other structures of the extracellular matrix. Some
collagens have about 15-18 vWA domains in them. The VWA
domains present in these collagens mediate
protein-protein interactions..
Length = 186
Score = 30.6 bits (69), Expect = 0.86
Identities = 32/153 (20%), Positives = 64/153 (41%), Gaps = 21/153 (13%)
Query: 259 VDSS----SLRHVIKKKHLVRDALASVIRSIKKIDNVNDTVRMGATFFNDRVISDPSFSW 314
+DSS I K + R +A + + R+G ++D+ + F
Sbjct: 9 LDSSESVGLQNFDITKNFVKR--VAERFLKDYYRKDPAGSWRVGVVQYSDQQEVEAGFLR 66
Query: 315 GVHKLIRTIVKTFAIDENEM--GSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIV 372
+ T +K A+D E G T + A++ A + ++ + + + K+++
Sbjct: 67 DIRN--YTSLKE-AVDNLEYIGGGTFTDCALKYATEQLLEGS---------HQKENKFLL 114
Query: 373 LLTDGENTQDNEEGI-AICNKAKSQGIRIMTIA 404
++TDG + + GI N+A GI+I +A
Sbjct: 115 VITDGHSDGSPDGGIEKAVNEADHLGIKIFFVA 147
>gnl|CDD|29245 cd01472, vWA_collagen, von Willebrand factor (vWF) type A domain;
equivalent to the I-domain of integrins. This domain
has a variety of functions including: intermolecular
adhesion, cell migration, signalling, transcription, and
DNA repair. In integrins these domains form heterodimers
while in vWF it forms homodimers and multimers. There
are different interaction surfaces of this domain as
seen by its complexes with collagen with either integrin
or human vWFA. In integrins collagen binding occurs via
the metal ion-dependent adhesion site (MIDAS) and
involves three surface loops located on the upper
surface of the molecule. In human vWFA, collagen binding
is thought to occur on the bottom of the molecule and
does not involve the vestigial MIDAS motif..
Length = 164
Score = 30.2 bits (68), Expect = 1.4
Identities = 28/134 (20%), Positives = 54/134 (40%), Gaps = 18/134 (13%)
Query: 273 LVRDALASVIRSIKKIDNVNDTVRMGATFFNDRVISDPSFSWGVHKLIRTIVKTFAIDEN 332
LV+D + V+ + D D VR+G ++D F ++ + A+
Sbjct: 20 LVKDFVKRVVERL---DIGPDGVRVGVVQYSDDPR--TEFYLNTYRSKDDV--LEAVKNL 72
Query: 333 EM--GSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLTDGENTQDNEEGIAIC 390
G T A++ + + + E + K +V++TDG+ +QD+ E A+
Sbjct: 73 RYIGGGTNTGKALKYVRENLFT----EASGSREG--VPKVLVVITDGK-SQDDVEEPAVE 125
Query: 391 NKAKSQGIRIMTIA 404
K GI + +
Sbjct: 126 --LKQAGIEVFAVG 137
>gnl|CDD|36639 KOG1425, KOG1425, KOG1425, Microfibrillar-associated protein MFAP1
[Cytoskeleton].
Length = 430
Score = 29.7 bits (66), Expect = 1.7
Identities = 28/136 (20%), Positives = 50/136 (36%), Gaps = 15/136 (11%)
Query: 330 DENEMGSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLTDGENTQDNEEGIAI 389
DE E + + ++ +T S +D R+K K+ L + E E+ +
Sbjct: 156 DEYESDEESEEEESESEEET--DSEDDMEPRLKPVFVRKRDRTTLQEREREAKKEKNLEK 213
Query: 390 CNKAKSQGIRIMT---IAFSVNKTQQEKARYFLSNCA----------SPNSFFEANSTHE 436
K ++ + T + V K + E+ + + + +EA E
Sbjct: 214 EAKRDAEERKRETLQIVEEEVIKKELEEKKTKNNEALLNDVDTDDEINEEEEYEAWKLRE 273
Query: 437 LNKIFRDRIGNEIFER 452
L +I RDR E ER
Sbjct: 274 LKRIKRDREEREELER 289
>gnl|CDD|39423 KOG4222, KOG4222, KOG4222, Axon guidance receptor Dscam [Signal
transduction mechanisms].
Length = 1281
Score = 29.3 bits (65), Expect = 2.2
Identities = 21/96 (21%), Positives = 32/96 (33%), Gaps = 22/96 (22%)
Query: 306 VISDPSFSWGVHKLIRTIVKTFAI-------DENEMGSTAINDAMQTAYDTIISSNEDEV 358
V++ P+F GVH+ IV F+I E G T S D +
Sbjct: 867 VVNQPAFIAGVHRACLIIVMVFSIIWLYWRRKEPLSGKDL----------TAGLSRLDNL 916
Query: 359 HRMKNNLEAKKYI-----VLLTDGENTQDNEEGIAI 389
N + K Y+ T + Q+ G +
Sbjct: 917 FTSLNVNQGKGYLPCYSPGWRTARLDHQNERAGQGL 952
>gnl|CDD|29250 cd01477, vWA_F09G8-8_type, VWA F09G8.8 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. The members of this subgroup lack the MIDAS
motif. This subgroup is found only in C. elegans and the
members identified thus far are always found fused to a
C-Lectin type domain. Biochemical function thus far has
not be attributed to any of the members of this
subgroup..
Length = 193
Score = 28.7 bits (64), Expect = 3.6
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 368 KKYIVLLTDGENTQDNEEGIAICNKAKSQGIRIMTIAFSVNKTQQEKARYFLSNCASPNS 427
KK +++ N + + + I + KS GI I+T+AF+ +++ + L ASP
Sbjct: 132 KKVVIVFASDYNDEGSNDPRPIAARLKSTGIAIITVAFTQDESSNLLDK--LGKIASPGM 189
Query: 428 FF 429
F
Sbjct: 190 NF 191
>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 = 28.7 bits (64), Expect = 3.8
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 366 EAKKYIVLLTDGENTQDNEEGIAICNKAKSQGIRIMTIA----FSVNKTQQE 413
+A K +V++TDGE+ D+ + +A+ +GI I F +++E
Sbjct: 102 DATKVLVVITDGESH-DDPLLKDVIPQAEREGIIRYAIGVGGHFQRENSREE 152
>gnl|CDD|109609 pfam00559, Vif, Retroviral Vif (Viral infectivity) protein. Human
immunodeficiency virus type 1 (HIV-1) Vif is required
for productive infection of T lymphocytes and
macrophages. Virions produced in the absence of Vif have
abnormal core morphology and those produced in primary T
cells carry immature core proteins and low levels of
mature capsid.
Length = 192
Score = 28.1 bits (63), Expect = 4.7
Identities = 19/82 (23%), Positives = 27/82 (32%), Gaps = 14/82 (17%)
Query: 154 KSWLIQTKAEAETVSRSYHKEHGVSIQWVIDFSRSMLD---YQRDSEGQPLNCFGQPADR 210
K L T R + + V IQW R+ +D G +CF +R
Sbjct: 61 KGKLEVQGYWHLTPERGWLSTYAVGIQWYSRKYRTEVDPDTADSLIHGHYFSCF---TER 117
Query: 211 TVKSYSSQNGKVGIRDEKLSPY 232
++ IR EKL
Sbjct: 118 AIRR--------AIRGEKLLSC 131
>gnl|CDD|153284 cd07600, BAR_Gvp36, The Bin/Amphiphysin/Rvs (BAR) domain of
Saccharomyces cerevisiae Golgi vesicle protein of 36 kDa
and similar proteins. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions including
organelle biogenesis, membrane trafficking or
remodeling, and cell division and migration. Proteomic
analysis shows that Golgi vesicle protein of 36 kDa
(Gvp36) may be involved in vesicular trafficking and
nutritional adaptation. A Saccharomyces cerevisiae
strain deficient in Gvp36 shows defects in growth, in
actin cytoskeleton polarization, in endocytosis, in
vacuolar biogenesis, and in the cell cycle. BAR domains
form dimers that bind to membranes, induce membrane
bending and curvature, and may also be involved in
protein-protein interactions.
Length = 242
Score = 28.1 bits (63), Expect = 5.1
Identities = 14/51 (27%), Positives = 23/51 (45%)
Query: 331 ENEMGSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLTDGENTQ 381
E A ++TA D +S+ E+ V MK L+ + + LL + Q
Sbjct: 174 EPAEKQEAARVEVETAEDEFVSATEEAVELMKEVLDNPEPLQLLKELVKAQ 224
>gnl|CDD|31953 COG1767, CitG, Triphosphoribosyl-dephospho-CoA synthetase [Coenzyme
metabolism].
Length = 288
Score = 28.0 bits (62), Expect = 5.5
Identities = 26/157 (16%), Positives = 46/157 (29%), Gaps = 27/157 (17%)
Query: 35 GVGGMLVDVVRWSYYEHALKQAAQTAIITASVPLIQSLEEVSSRAK-NSFTFPKQKIEEY 93
+G +L D + E A+ I T PLI + + A ++
Sbjct: 73 DLGALLRDAGLEA--EKAMFGNTNFGINTLLKPLIFAAGLGNLCAAAGRLLARTTPLDAV 130
Query: 94 LIRNFENNLKKNFTDREVRDIVRDTAVEMNPRK-----------------------SAYQ 130
+ + RE++ V D + ++
Sbjct: 131 ELCDAIKQACAGLVKRELKADVSDETAGERLFRKYGLLGARGEAASGFPLVRSHALPGFK 190
Query: 131 VVLSSRYDLLLNPLSLFLRSMGIKS-WLIQTKAEAET 166
+L DL L L+ + I S LI ++ AE
Sbjct: 191 RLLEGGLDLERALLQTLLKLLAINSDTLIASRGGAEG 227
>gnl|CDD|29237 cd01464, vWA_subfamily, VWA subfamily: 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 have no assigned
function. This subfamily is typified by the presence of
a conserved MIDAS motif..
Length = 176
Score = 27.9 bits (62), Expect = 6.0
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 335 GSTAINDAMQTAYDTIISSNEDEVHRMKNNLEA--KKYIVLLTDGENTQDNEEGIAICNK 392
G T++ A++ A D I + V R + + + + ++ LLTDGE T D I +
Sbjct: 77 GGTSMGAALELALDCI----DRRVQRYRADQKGDWRPWVFLLTDGEPTDDLTAAIERIKE 132
Query: 393 AKSQGIRIMTIAFSVN 408
A+ RI+ A
Sbjct: 133 ARDSKGRIVACAVGPK 148
>gnl|CDD|80364 cd04821, PA_M28_1_2, PA_M28_1_2: Protease-associated (PA) domain,
peptidase family M28, subfamily-1, subgroup 2. A
subgroup of PA-domain containing proteins belonging to
the peptidase family M28. Family M28 contains
aminopeptidases and carboxypeptidases, and has
co-catalytic zinc ions. The PA domain is an insert
domain in a diverse fraction of proteases. The
significance of the PA domain to many of the proteins
in which it is inserted is undetermined. It may be a
protein-protein interaction domain. At peptidase active
sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site
to substrate. Proteins into which the PA domain is
inserted include the following members of the peptidase
family M28: i) prostate-specific membrane antigen
(PSMA), ii) yeast aminopeptidase Y, and ii) human TfR
(transferrin receptor)1 and human TfR2. The proteins
listed above belong to other subgroups; relatively
little is known about proteins in this subgroup..
Length = 157
Score = 27.9 bits (62), Expect = 6.3
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 45 RWSY-YEHALKQAAQTAII 62
RW+Y YE A +Q A A+I
Sbjct: 80 RWTYKYEEAARQGAAGALI 98
>gnl|CDD|32614 COG2721, UxaA, Altronate dehydratase [Carbohydrate transport and
metabolism].
Length = 381
Score = 27.9 bits (62), Expect = 6.4
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 206 QPADRTVKSYSSQNGKVGIRDE 227
A+RT + Y +G+VG R+E
Sbjct: 1 PAAERTFQGYRRADGRVGTRNE 22
>gnl|CDD|32386 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 27.6 bits (61), Expect = 8.5
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 10/54 (18%)
Query: 240 LYYMLYPGPLD-PSLSE---------EHFVDSSSLRHVIKKKHLVRDALASVIR 283
LYY L PL P L E EHF+ + K +ALA+++
Sbjct: 300 LYYRLNVVPLRLPPLRERKEDIPLLAEHFLKRFAAELGRPPKGFSPEALAALLA 353
>gnl|CDD|33640 COG3850, NarQ, Signal transduction histidine kinase,
nitrate/nitrite-specific [Signal transduction
mechanisms].
Length = 574
Score = 27.2 bits (60), Expect = 8.9
Identities = 38/228 (16%), Positives = 71/228 (31%), Gaps = 36/228 (15%)
Query: 49 YEHALKQAAQTAIITASVPL-----IQSLEEVSSRAKNSFTFPKQKIEEYL--IRNFENN 101
++ +L A A++ VPL Q L R + Y + +F
Sbjct: 72 FQTSLHSPALRALLPWRVPLAVKTQYQQLIA-YWRNMLKPLLLQGDRRPYQADLADFVAQ 130
Query: 102 LKKNFTDREVRDIVRDTAVEMNPRKSAYQVVLSSRYDLLLNPLSLFLRSMGIKSWLIQTK 161
+ D+ V + R + +VL +LL L + ++ +++
Sbjct: 131 I-----DQFVLALQRFAE------RKTILLVLVQLAGMLLILLLVVFTIYWLRRRVVRPL 179
Query: 162 AEAETVSRSYHKEHGVSIQWVIDFSRSMLDYQRDSEGQPLNCFGQPADRTVKSYSSQNGK 221
+ + ++ F + D R+ G F Q + K Y+ +
Sbjct: 180 NQLTSAAQRI--GRR-------QFDQRPTDTGRNELGLLGRAFNQMSGELKKLYADLEQR 230
Query: 222 VGIRDEKLSPYMVSCNKSLYYMLYPGPLDPSLSEEHFVDSSSLRHVIK 269
V + L N+ L LY +D LRHV+
Sbjct: 231 VEEKTRDLE----QKNQRL-SFLYQSSRRLH---TSQIDDERLRHVLN 270
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
0.319 0.133 0.378
Gapped
Lambda K H
0.267 0.0793 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,357,468
Number of extensions: 276656
Number of successful extensions: 735
Number of sequences better than 10.0: 1
Number of HSP's gapped: 733
Number of HSP's successfully gapped: 32
Length of query: 458
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 361
Effective length of database: 4,167,664
Effective search space: 1504526704
Effective search space used: 1504526704
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.4 bits)