RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13343
(396 letters)
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include SRY and its homologs in insects and
vertebrates, and transcription factor-like proteins,
TCF-1, -3, -4, and LEF-1. They appear to bind the minor
groove of the A/T C A A A G/C-motif.
Length = 72
Score = 125 bits (315), Expect = 1e-35
Identities = 37/72 (51%), Positives = 53/72 (73%)
Query: 82 RVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
+KRPMNAFM++S+ RRK+ Q+ P N ISK LG WK L+ + K+P+ +EAK+L+
Sbjct: 1 HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKE 60
Query: 142 VHMKEHPDYKYR 153
+HMK +PDYK+R
Sbjct: 61 LHMKLYPDYKWR 72
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 101 bits (253), Expect = 9e-27
Identities = 30/69 (43%), Positives = 51/69 (73%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
KRP++AF ++S+ QR K+ +NP + N+EISK LG +WK L+E+ K+P+ ++A++ +A
Sbjct: 1 PKRPLSAFFLFSQEQRAKLKAENPGLKNAEISKILGEKWKNLSEEEKKPYEEKAEKEKAR 60
Query: 143 HMKEHPDYK 151
+ K +P YK
Sbjct: 61 YEKAYPAYK 69
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 92.8 bits (231), Expect = 1e-23
Identities = 32/70 (45%), Positives = 52/70 (74%)
Query: 82 RVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
+ KRPM+AFM++S+ R K+ +NP + N+EISK+LG WKLL+E+ K P+ ++AK+ +
Sbjct: 1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
Query: 142 VHMKEHPDYK 151
+ +E P+YK
Sbjct: 61 RYEEEMPEYK 70
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a
variety of eukaryotic chromosomal proteins and
transcription factors. HMGs bind to the minor groove of
DNA and have been classified by DNA binding preferences.
Two phylogenically distinct groups of Class I proteins
bind DNA in a sequence specific fashion and contain a
single HMG box. One group (SOX-TCF) includes
transcription factors, TCF-1, -3, -4; and also SRY and
LEF-1, which bind four-way DNA junctions and duplex DNA
targets. The second group (MATA) includes fungal mating
type gene products MC, MATA1 and Ste11. Class II and III
proteins (HMGB-UBF) bind DNA in a non-sequence specific
fashion and contain two or more tandem HMG boxes. Class
II members include non-histone chromosomal proteins,
HMG1 and HMG2, which bind to bent or distorted DNA such
as four-way DNA junctions, synthetic DNA cruciforms,
kinked cisplatin-modified DNA, DNA bulges, cross-overs
in supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 85.0 bits (211), Expect = 9e-21
Identities = 23/66 (34%), Positives = 43/66 (65%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
KRP++A+ ++S+ R ++ +NP + EISK LG WK L+E+ K+ + ++A++ +
Sbjct: 1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKER 60
Query: 143 HMKEHP 148
+ KE P
Sbjct: 61 YEKEMP 66
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box
superfamily of DNA-binding proteins. These proteins
contain a single HMG box, and bind the minor groove of
DNA in a highly sequence-specific manner. Members
include the fungal mating type gene products MC, MATA1
and Ste11.
Length = 77
Score = 74.6 bits (184), Expect = 5e-17
Identities = 24/76 (31%), Positives = 48/76 (63%)
Query: 82 RVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
++ RP NAF+++ + + ++ +NP + N+EIS+ +G W+ + + K + + A+ +
Sbjct: 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKE 60
Query: 142 VHMKEHPDYKYRPRRK 157
H +E+PDYKY PR+
Sbjct: 61 RHAREYPDYKYTPRKS 76
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III
members of the HMG-box superfamily of DNA-binding
proteins. These proteins bind the minor groove of DNA in
a non-sequence specific fashion and contain two or more
tandem HMG boxes. Class II members include non-histone
chromosomal proteins, HMG1 and HMG2, which bind to bent
or distorted DNA such as four-way DNA junctions,
synthetic DNA cruciforms, kinked cisplatin-modified DNA,
DNA bulges, cross-overs in supercoiled DNA, and can
cause looping of linear DNA. Class III members include
nucleolar and mitochondrial transcription factors, UBF
and mtTF1, which bind four-way DNA junctions.
Length = 66
Score = 67.3 bits (165), Expect = 2e-14
Identities = 22/63 (34%), Positives = 45/63 (71%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
KRP++A+ ++S+ QR K+ ++NP +E++K LG +WK L+E+ K+ + ++A++ + +
Sbjct: 2 KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERY 61
Query: 144 MKE 146
KE
Sbjct: 62 EKE 64
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 56.8 bits (137), Expect = 2e-09
Identities = 22/68 (32%), Positives = 40/68 (58%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
KRP++A+ ++S R ++ ++NPK+ E+ K L +WK L ++ K P+ EA R +
Sbjct: 72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERY 131
Query: 144 MKEHPDYK 151
+E +Y
Sbjct: 132 QREKEEYN 139
Score = 29.1 bits (65), Expect = 2.9
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 105 NPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPD 149
+P E +K + W L+E K+ +ID+ K+L+ + +P+
Sbjct: 166 SPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYPE 210
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898). This
domain is predominantly found in Maelstrom homolog
proteins. It has no known function.
Length = 69
Score = 42.4 bits (100), Expect = 1e-05
Identities = 13/61 (21%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 82 RVKRPMNAFMVWSRGQRRKMAQDNPKMHN-SEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
+ K NA+ + + R ++ ++ P++ +E SK +WK ++E+ K + ++A+ +
Sbjct: 3 KPKAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEKAREDK 62
Query: 141 A 141
Sbjct: 63 K 63
>gnl|CDD|152771 pfam12336, SOXp, SOX transcription factor. This domain family is
found in eukaryotes, and is approximately 80 amino acids
in length. The family is found in association with
pfam00505. There are two conserved sequence motifs: KKDK
and LPG. This family is made up of SOX transcription
factors. These are involved in upregulation of nestin, a
neural promoter.
Length = 84
Score = 41.4 bits (97), Expect = 5e-05
Identities = 33/99 (33%), Positives = 38/99 (38%), Gaps = 19/99 (19%)
Query: 152 YRPRRKTKTLLKKDKYPLGSGNLIQNTSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNG 211
YRPRRKTKTLLKKDKY L G L N + Q+ Y NG
Sbjct: 1 YRPRRKTKTLLKKDKYSLPGGLLPANGAPV--------------QRAVGVGMDGYAHMNG 46
Query: 212 YMPNGYMMDPATYQQHSAYTTH--MSSGYPRYDMTGMHP 248
YM Y M Y H M+S + +H
Sbjct: 47 YMNGAYSMMQ---DDQLHYPQHPGMNSAQAQQANQQLHH 82
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional.
Length = 94
Score = 38.7 bits (90), Expect = 4e-04
Identities = 22/83 (26%), Positives = 46/83 (55%), Gaps = 5/83 (6%)
Query: 70 NSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHN--SEISKRLGAEWKLLNEQ 127
N K+ NA KR ++A+M +++ +R ++ +NP++ + + K +G W L+E+
Sbjct: 13 NKRKKKDPNA---PKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEE 69
Query: 128 AKRPFIDEAKRLRAVHMKEHPDY 150
K P+ +A+ + + KE +Y
Sbjct: 70 EKAPYEKKAQEDKVRYEKEKAEY 92
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 34.7 bits (80), Expect = 0.061
Identities = 20/114 (17%), Positives = 30/114 (26%), Gaps = 4/114 (3%)
Query: 271 LPGAGSPYHSMQPSSHSPSGSSVKSEPVSP-SSGGGILTPTPGSGPPTGLHLVKREYGSP 329
+ P S SP S S P P S L P P S +P
Sbjct: 175 EDADPASASPSDPPSSSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNP 234
Query: 330 NGLPPNSTDLHLVKREYSSPNGAPPNAGDLRHMISMYLPEQQEQARLQAMYQQQ 383
+ P + ++ + A P + P A+ + Q
Sbjct: 235 SPPPGPAAPPPPPVQQVPPLSTAKPTP---PSASATPAPIGGITLDDDAIAKAQ 285
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 32.2 bits (73), Expect = 0.48
Identities = 31/204 (15%), Positives = 64/204 (31%), Gaps = 45/204 (22%)
Query: 222 ATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTAT-----TLPGAGS 276
+ ++ ++ H S ++ H + + +S S + ++ ++ S
Sbjct: 271 HSIGINNHHSKHADSKLQTIEVIENHSNKSRPSSSSTNGSKETTSNSSSAAAGSIGSKSS 330
Query: 277 PYHSM--------QPSSHSPSGSSVKSEPVS---------PSSGGGILTPTPGSGPPTGL 319
P SHS + SV S VS S G + +
Sbjct: 331 KSAKHSNRNKSNSSPKSHSSANGSVPSSSVSDNESKQKRASKSSSGARDSKKDASGMSAN 390
Query: 320 HLVKRE-----YGSPNGLPPNSTDLHLVKREYSSPNGAPPNAGDLRHMISMY-------- 366
V+ +P+ + D+ ++ E A N +LR+ IS+
Sbjct: 391 GTVENCIPENKISTPSAIERLEQDIKKLQAELQQ---ARQNESELRNQISLLTSLERSLK 447
Query: 367 ---LPEQQE----QARLQAMYQQQ 383
++E Q +L +M +
Sbjct: 448 SDLGQLKKENDMLQTKLNSMVSAK 471
>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 617
Score = 30.9 bits (70), Expect = 1.3
Identities = 13/46 (28%), Positives = 15/46 (32%)
Query: 272 PGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSGPPT 317
PGAG + V P +P P PG G PT
Sbjct: 233 PGAGHVHRGGPGPPERDDAPVVPIRPSAPGPLAAQPAPAPGPGEPT 278
>gnl|CDD|133084 cd06226, M14_CPT_like, Peptidase M14 Carboxypeptidase T-like
subfamily. Peptidase M14-like domain of an
uncharacterized group of Peptidase M14 Carboxypeptidase
(CP) T (CPT)-like proteins. This group belongs to the
M14 family of metallocarboxypeptidases (MCPs). The M14
family are zinc-binding CPs which hydrolyze single,
C-terminal amino acids from polypeptide chains, and have
a recognition site for the free C-terminal carboxyl
group, which is a key determinant of specificity. CPT
exhibits dual-substrate specificity by cleaving
C-terminal hydrophobic amino acid residues and
C-terminal positively charged residues. However, CPT
does not belong to this CPT-like group.
Length = 293
Score = 30.1 bits (68), Expect = 1.8
Identities = 35/131 (26%), Positives = 49/131 (37%), Gaps = 27/131 (20%)
Query: 251 TSLNSYMNGSSYGM-----YTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGG 305
TS S +GSSYG+ Y+ GA S P S + G + SEP + +
Sbjct: 114 TSGGSNCSGSSYGVDLNRNYSFGWGGAGASSGD----PCSETYRGPAPGSEPETAALEDY 169
Query: 306 ILTPTPGSGPP----------TGLH--------LVKREYGSPNGLPPNSTDLHLVKREYS 347
I P P TG++ LV +G PN T L + R+++
Sbjct: 170 IRGLFPDQRGPGDTDPAPDDTTGVYLDIHSYSNLVLYPWGWTTQPAPNDTQLRALGRKFA 229
Query: 348 SPNGAPPNAGD 358
S NG P
Sbjct: 230 SFNGYTPQQSV 240
>gnl|CDD|226067 COG3537, COG3537, Putative alpha-1,2-mannosidase [Carbohydrate
transport and metabolism].
Length = 768
Score = 30.5 bits (69), Expect = 2.0
Identities = 17/68 (25%), Positives = 22/68 (32%), Gaps = 16/68 (23%)
Query: 270 TLPGAGSPYHSMQPS-------------SHSP-SGSSVKSEPVSPSSG--GGILTPTPGS 313
T PGAG P+ +Q S P G S+ + P G + T TP
Sbjct: 59 TFPGAGVPFGMVQLSPDTVDADAGWGYDPAPPIMGFSMTHQSGCPGFGDYSMLPTTTPVG 118
Query: 314 GPPTGLHL 321
P
Sbjct: 119 SPLWSAWE 126
>gnl|CDD|202199 pfam02305, Phage_F, Capsid protein (F protein). This is a family
of proteins from single-stranded DNA bacteriophages.
Protein F is the major capsid component, sixty copies of
which are found in the virion.
Length = 450
Score = 29.8 bits (67), Expect = 3.0
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 14/76 (18%)
Query: 180 SSNDVTRNSSSVTTSAQQNSAA------RESMYQMPNGYMPNGYMMD------PATYQQH 227
S DV + SS+ + S Q N AA + + + +P ++ +G ++ P TYQQ
Sbjct: 258 SGYDVPQTSSTDSKSPQGNLAAFSGRVQQTNKHLVPKFFVEHGVIITLAVVRFPPTYQQG 317
Query: 228 SAYTTHMSSGYPRYDM 243
Y S G YD+
Sbjct: 318 LHYL--WSRGQLTYDI 331
>gnl|CDD|183454 PRK12341, PRK12341, putative acyl-CoA dehydrogenase; Provisional.
Length = 381
Score = 29.3 bits (66), Expect = 3.4
Identities = 20/68 (29%), Positives = 26/68 (38%), Gaps = 5/68 (7%)
Query: 322 VKREYGSPNGLPPNSTDLHLVKREYSSPNGAPPNA-GDLRHMISMYLPEQQEQARLQAMY 380
V E+G G P + LV E S GAP + + + SM EQ R A
Sbjct: 56 VPEEFG---GTPADYVTQMLVLEEVSK-CGAPAFLITNGQCIHSMRRFGSAEQLRKTAES 111
Query: 381 QQQAGHPP 388
+ G P
Sbjct: 112 TLETGDPA 119
>gnl|CDD|184262 PRK13706, PRK13706, conjugal transfer pilus acetylation protein
TraX; Provisional.
Length = 248
Score = 29.2 bits (65), Expect = 3.8
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 65 TNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQR 98
T +N N+T +N + R + + +VWS GQR
Sbjct: 2 TTDNTNTT--RNDSLAARTDTWLQSLLVWSPGQR 33
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 29.5 bits (66), Expect = 4.0
Identities = 32/145 (22%), Positives = 56/145 (38%), Gaps = 14/145 (9%)
Query: 154 PRRKTKTLLKKDKYPLGSGNLIQNTSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYM 213
P +K K L G+ I + +N + + + + S +SM Q+P+
Sbjct: 140 PVQKRKNPLLPSSSTHGTHPPI-VFTDNNGSHAGAPNARSRKEIPSLGSQSM-QLPS--- 194
Query: 214 PNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPG 273
P Q+ S+ T YP H SS S+ S+ + S+ + + G
Sbjct: 195 -------PHFRQKFSSSDTSNGFSYPSIRKNSRH-SSNSMPSFPHSSTAVLLKRHSGSSG 246
Query: 274 AGSPYHSMQPSS-HSPSGSSVKSEP 297
A ++ PSS +S + S+ P
Sbjct: 247 ASLISSNITPSSSNSEAMSTSSKRP 271
>gnl|CDD|235599 PRK05769, PRK05769, 4-aminobutyrate aminotransferase; Provisional.
Length = 441
Score = 29.1 bits (66), Expect = 4.3
Identities = 16/59 (27%), Positives = 20/59 (33%), Gaps = 11/59 (18%)
Query: 18 HLSSYGSMVHSNMMSLSQSPSSVVHHQNIGP---HVTHNPMSNPLHPSHNTNNNNNSTN 73
H +YGS+ SL+ S V + P V H P NP N N
Sbjct: 152 HGRTYGSL------SLTASKP--VQRKGFFPLMPGVIHVPYPNPYRNPWGIENPEECGN 202
>gnl|CDD|193227 pfam12751, Vac7, Vacuolar segregation subunit 7. Vac7 is localised
at the vacuole membrane, a location which is consistent
with its involvement in vacuole morphology and
inheritance. Vac7 has been shown to function as an
upstream regulator of the Fab1 lipid kinase pathway. The
Fab1 lipid kinase pathway is important for correct
regulation of membrane trafficking events.
Length = 386
Score = 29.1 bits (65), Expect = 4.5
Identities = 15/79 (18%), Positives = 26/79 (32%), Gaps = 5/79 (6%)
Query: 5 ETDLKGGHIPPHHHLSSYGSMVHSNMMSL--SQSPSSVVH-HQNIGPHVTHNPMSNPLHP 61
++ G H P HHH+ +G + SL + SP H N
Sbjct: 170 RSNGHGTHTPRHHHIGRHGR--NGGHPSLFDNDSPFPQSQKSPKSPRHFIGNGSRQSRRG 227
Query: 62 SHNTNNNNNSTNSKNQNAI 80
+ +N N + ++
Sbjct: 228 TPRSNPNYRTIGGPKKSGD 246
>gnl|CDD|216455 pfam01364, Peptidase_C25, Peptidase family C25.
Length = 340
Score = 28.8 bits (65), Expect = 4.8
Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 19/92 (20%)
Query: 198 NSAARESMYQMPNGYMPNGYMMDPATYQQHSA---------------YTTHMSSGYPRYD 242
+S A +P+GY N D Y+ + YT H G
Sbjct: 163 DSLADTIAALLPDGYNVNKIYADAYAYESAARQNILDALNQGALIVNYTGH---GSETGW 219
Query: 243 MTGMHPSSTSLNSYMNGSSYGMYTTATTLPGA 274
++T + + NG+ + TAT L G
Sbjct: 220 ADE-GLTATDVKNLTNGNKLPLVITATCLTGR 250
>gnl|CDD|131451 TIGR02398, gluc_glyc_Psyn, glucosylglycerol-phosphate synthase.
Glucosylglycerol-phosphate synthase catalyzes the key
step in the biosynthesis of the osmolyte
glucosylglycerol. It is known in several cyanobacteria
and in Pseudomonas anguilliseptica. The enzyme is
closely related to the alpha,alpha-trehalose-phosphate
synthase, likewise involved in osmolyte biosynthesis, of
E. coli and many other bacteria. A close homolog from
Xanthomonas campestris is excluded from this model and
scores between trusted and noise.
Length = 487
Score = 28.7 bits (64), Expect = 6.9
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 14/74 (18%)
Query: 318 GLHLVKREYGSPNGLPPNSTDLHLVKREYSS-----PNGAPPNAGDLRHM-----ISMYL 367
GL+LV +EY + GL D LV E++ N D M +++ +
Sbjct: 393 GLNLVAKEYVAAQGL----LDGVLVLSEFAGAAVELKGALLTNPYDPVRMDETIYVALAM 448
Query: 368 PEQQEQARLQAMYQ 381
P+ ++QAR++ M+
Sbjct: 449 PKAEQQARMREMFD 462
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 28.6 bits (64), Expect = 7.5
Identities = 26/129 (20%), Positives = 36/129 (27%), Gaps = 10/129 (7%)
Query: 196 QQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYP-RYDMTGMHPSSTSLN 254
Q + M Q+P G G M P Y Q +G P + M P+
Sbjct: 373 DQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQ---QQFNGQPLGWPRMSMMPTP---- 425
Query: 255 SYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSG 314
G + +P + Q ++ P V P S P P S
Sbjct: 426 MGPGGPLRPN--GLAPMNAVRAPSRNAQNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQST 483
Query: 315 PPTGLHLVK 323
G K
Sbjct: 484 ASQGGQNKK 492
>gnl|CDD|227661 COG5366, COG5366, Protein involved in propagation of M2 dsRNA
satellite of L-A virus [General function prediction
only].
Length = 531
Score = 28.0 bits (62), Expect = 9.3
Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 3/55 (5%)
Query: 173 NLIQNTSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYMPNGYM-MDPATYQQ 226
N +Q TSS T +S Q+N +++ N M M + ++
Sbjct: 88 NKLQGTSSGGLGTLLTSGFKEYTQENYRKAGKLWR--NFIMQKSEMDVASKILEE 140
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
0.310 0.124 0.369
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,491,015
Number of extensions: 1771527
Number of successful extensions: 1557
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1519
Number of HSP's successfully gapped: 75
Length of query: 396
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 297
Effective length of database: 6,546,556
Effective search space: 1944327132
Effective search space used: 1944327132
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 60 (27.1 bits)